From 4d00002daec95664cd88a1ac987b91df3d28e71d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 02:08:06 +0200
Subject: [PATCH 01/20] Update cutadapt first round
---
tools/cutadapt/cutadapt.xml | 314 +++++++++++-------
tools/cutadapt/macros.xml | 50 ++-
tools/cutadapt/test-data/A1.fastq.gz | Bin 348 -> 340 bytes
tools/cutadapt/test-data/A2.fastq.gz | Bin 334 -> 326 bytes
.../test-data/cutadapt_nextseq_out.fq.gz | Bin 11712 -> 12158 bytes
tools/cutadapt/test-data/cutadapt_out1.fq.gz | Bin 11934 -> 54684 bytes
tools/cutadapt/test-data/cutadapt_out2.fq.gz | Bin 12009 -> 54666 bytes
.../cutadapt/test-data/cutadapt_small_cut.out | 12 +
.../test-data/cutadapt_small_rename.out | 12 +
.../test-data/cutadapt_trimmed.out.gz | Bin 537 -> 537 bytes
.../test-data/cutadapt_untrimmed.out.gz | Bin 11648 -> 12095 bytes
tools/cutadapt/test-data/unknown.fastq.gz | Bin 191 -> 173 bytes
12 files changed, 247 insertions(+), 141 deletions(-)
create mode 100644 tools/cutadapt/test-data/cutadapt_small_cut.out
create mode 100644 tools/cutadapt/test-data/cutadapt_small_rename.out
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index aebcd3d2d6a..1fb98d550b6 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -1,12 +1,11 @@
-<tool id="cutadapt" name="Cutadapt" version="1.16.9" profile="17.09">
+<tool id="cutadapt" name="Cutadapt" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
<description>Remove adapter sequences from Fastq/Fasta</description>
<macros>
<import>macros.xml</import>
</macros>
- <requirements>
- <requirement type="package" version="1.16">cutadapt</requirement>
- </requirements>
-
+ <expand macro='edam_ontology' />
+ <expand macro='requirements' />
+ <expand macro='xrefs'/>
<version_command>cutadapt --version</version_command>
<command detect_errors="exit_code"><![CDATA[
@@ -18,20 +17,20 @@
#set paired = False
#set library_type = str($library.type)
#if $library_type == 'paired':
-#set paired = True
-#set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
-#set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
-#set input_1 = $library.input_1
-#set input_2 = $library.input_2
+ #set paired = True
+ #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
+ #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
+ #set input_1 = $library.input_1
+ #set input_2 = $library.input_2
#else if $library_type == 'paired_collection'
-#set paired = True
-#set input_1 = $library.input_1.forward
-#set input_2 = $library.input_1.reverse
-#set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_1"
-#set read2 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_2"
+ #set paired = True
+ #set input_1 = $library.input_1.forward
+ #set input_2 = $library.input_1.reverse
+ #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_1"
+ #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_2"
#else
-#set input_1 = $library.input_1
-#set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
+ #set input_1 = $library.input_1
+ #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
#end if
#if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
@@ -72,20 +71,17 @@ ln -f -s '${input_1}' '$read1' &&
## Run Cutadapt
-#if $output_options.multiple_output:
+#if 'multiple_output' in $output_selector:
mkdir split &&
#end if
cutadapt
-## cutadapt (up to version 1.16) can't be run in multicore mode with these options
-#if not any(($output_options.info_file, $output_options.rest_file, $output_options.wildcard_file, $output_options.too_short_file, $output_options.too_long_file, $output_options.untrimmed_file))
- -j \${GALAXY_SLOTS:-1}
-#end if
+-j=\${GALAXY_SLOTS:-1}
#if str( $library.type ) == "single":
@read1_options@
- #if $output_options.multiple_output:
+ #if 'multiple_output' in $output_selector:
--output='split/{name}.${input_1.ext}'
#else:
--output='$out1'
@@ -103,20 +99,25 @@ cutadapt
#end if
--error-rate=$adapter_options.error_rate
---times=$adapter_options.count
+--times=$adapter_options.times
--overlap=$adapter_options.overlap
$adapter_options.no_indels
$adapter_options.match_read_wildcards
-$adapter_options.no_trim
-$adapter_options.mask_adapter
+--action=$adapter_options.action
+$adapter_options.revcomp
-$filter_options.discard
+$filter_options.discard_trimmed
$filter_options.discard_untrimmed
-#if str($filter_options.min):
- --minimum-length=$filter_options.min
+
+#if str($filter_options.minimum_options.minimum_r2):
+ --minimum-length=$filter_options.minimum_length:$filter_options.minimum_options.value_minimum
+#elif str($filter_options.minimum_length)
+ --minimum-length=$filter_options.minimum_length
#end if
-#if str($filter_options.max):
- --maximum-length=$filter_options.max
+#if str($filter_options.maximum_options.maximum_r2):
+ --maximum-length=$filter_options.maximum_length:$filter_options.maximum_options.value_maximum
+#elif str($filter_options.maximum_length)
+ --maximum-length=$filter_options.maximum_length
#end if
#if str($filter_options.max_n):
--max-n=$filter_options.max_n
@@ -126,6 +127,9 @@ $filter_options.discard_untrimmed
--pair-filter=$filter_options.pair_filter
#end if
#end if
+#if str($filter_options.max_expected_errors):
+ --max-expected-errors=$filter_options.max_expected_errors
+#end if
#if str($read_mod_options.quality_cutoff) != '0':
@@ -135,25 +139,27 @@ $filter_options.discard_untrimmed
--nextseq-trim=$read_mod_options.nextseq_trim
#end if
$read_mod_options.trim_n
-#if $read_mod_options.prefix != '':
- --prefix='$read_mod_options.prefix'
-#end if
-#if $read_mod_options.suffix != '':
- --suffix='$read_mod_options.suffix'
-#end if
#if str($read_mod_options.length) != '0':
--length=$read_mod_options.length
#end if
#if $read_mod_options.length_tag != '':
--length-tag='$read_mod_options.length_tag'
#end if
+#if $read_mod_options.cut != '0':
+ --cut=$read_mod_options.cut
+#end if
+#if $read_mod_options.rename != '':
+ --rename='$read_mod_options.rename'
+#end if
+$read_mod_options.zero_cap
+
'${read1}'
#if $paired:
'${read2}'
#end if
-#if $output_options.report:
+#if 'report' in $output_selector:
> report.txt
#end if
]]></command>
@@ -187,128 +193,157 @@ $read_mod_options.trim_n
<!-- Adapter Options -->
<section name="adapter_options" title="Adapter Options">
- <param name="error_rate" argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
- <param name="no_indels" argument="--no-indels" type="boolean" value="False" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
- <param name="count" argument="--times" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
- <param name="overlap" argument="--overlap" type="integer" min="1" value="3" label="Minimum overlap length" help="Minimum overlap length. If the overlap between the adapter and the sequence is shorter than LENGTH, the read is not modified. This reduces the number of bases trimmed purely due to short random adapter matches." />
+ <param name="action" type="select" label="What to do if a match is found">
+ <option value="trim" selected="True">Trim: trim adapter and upstream or downstream sequence</option>
+ <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option>
+ <option value="mask">Mask: madapters with 'N' characters instead of trimming them</option>
+ <option value="lowercase">Lowercase: convert to lowercase</option>
+ <option value="none">None: leave unchanged</option>
+ </param>
+ <param argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
+ <param argument="--no-indels" type="boolean" value="False" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
+ <param argument="--times" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
+ <param argument="--overlap" type="integer" min="1" value="3" label="Minimum overlap length" help="Minimum overlap length. If the overlap between the adapter and the sequence is shorter than LENGTH, the read is not modified. This reduces the number of bases trimmed purely due to short random adapter matches." />
<param name="match_read_wildcards" type="select" label="Match Wildcards" help="Allow 'N's as matches. Default: In the adapters but not in the reads">
<option value=" " selected="True">In the adapters but not in the reads</option>
<option value="--match-read-wildcards">In the adapters and in the reads</option>
<option value="--no-match-adapter-wildcards">Nowhere</option>
</param>
- <param name="no_trim" argument="--no-trim" type="boolean" value="False" truevalue="--no-trim" falsevalue="" label="Do not trim adapters" help="Match and redirect reads to output/untrimmed-output as usual, but don't remove the adapters (default: trim the adapters)." />
- <param name="mask_adapter" argument="--mask-adapter" type="boolean" value="False" truevalue="--mask-adapter" falsevalue="" label="Mask Adapters" help="Mask adapter bases with 'N' instead of trimming them (default: trim adapters)." />
+ <param argument="--revcomp" type="boolean" value="False" truevalue="--revcomp" falsevalue="" label="Look for adapters in the reverse complement" help="Check both the read and its reverse complement for adapter matches. If match is on reverse-complemented version, output that one. Default: check only read." />
+
</section>
<!-- Filter Options -->
<section name="filter_options" title="Filter Options">
- <param name="discard" argument="--discard-trimmed" type="boolean" value="False" truevalue="--discard-trimmed" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />
- <param name="discard_untrimmed" argument="--discard_untrimmed" type="boolean" value="False" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." />
- <param name="min" argument="--minimum-length" type="integer" min="0" optional="True" value="" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
- <param name="max" argument="--maximum-length" type="integer" min="0" optional="True" value="" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
- <param name="max_n" argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
- <param name="pair_filter" argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
+ <param argument="--discard-trimmed" type="boolean" value="False" truevalue="--discard-trimmed" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />
+ <param argument="--discard_untrimmed" type="boolean" value="False" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." />
+ <param argument="--minimum-length" type="integer" min="0" optional="True" value="" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
+ <conditional name="minimum_options">
+ <param name="minimum_r2" type="select" label="Specify a minimum length for reverse reads (R2)" help="When trimming paired-end reads, the minimum lengths for R1 and R2 can be specified separately. If not provided, the same minimum length applies to both reads.">
+ <option value="true">Enable</option>
+ <option value="" selected="True">Disable</option>
+ </param>
+ <when value="true">
+ <param name="value_minimum" type="integer" min="0" optional="True" value="" label="Minimum length" />
+ </when>
+ <when value="">
+ </when>
+ </conditional>
+ <param argument="--maximum-length" type="integer" min="0" optional="True" value="" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
+ <conditional name="maximum_options">
+ <param name="maximum_r2" type="select" label="Specify a maximum length for reverse reads (R2)" help="When trimming paired-end reads, the maximum lengths for R1 and R2 can be specified separately. If not provided, the same maximum length applies to both reads.">
+ <option value="true">Enable</option>
+ <option value="" selected="True">Disable</option>
+ </param>
+ <when value="true">
+ <param name="value_maximum" type="integer" min="0" optional="True" value="" label="Maximum length" />
+ </when>
+ <when value="">
+ </when>
+ </conditional>
+ <param argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
+ <param argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
<option value="any" selected="True">any</option>
<option value="both">both</option>
</param>
+ <param argument="--max-expected-errors" type="integer" min="0" optional="True" value="" label="Max expected errors" help="Discard reads whose expected number of errors (computed from quality values) exceeds this value." />
+ <param argument="--discard-cassava" type="boolean" truevalue="--discard-cassava" falsevalue="" checked="False" label="Discard CASAVA filtering" help="Discard reads that did not pass CASAVA filtering (header has :Y:)." />
</section>
<!-- Read Modification Options -->
<section name="read_mod_options" title="Read Modification Options">
- <param name="quality_cutoff" argument="--quality-cutoff" type="text" value="0" label="Quality cutoff" help=" Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads if data is paired. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second.">
+ <param argument="--quality-cutoff" type="text" value="0" label="Quality cutoff" help=" Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads if data is paired. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second.">
<sanitizer>
<valid initial="string.digits"><add value="," /></valid>
</sanitizer>
</param>
- <param name="nextseq_trim" argument="--nextseq-trim" type="integer" value="0" label="NextSeq trimming" help="Experimental option for quality trimming of NextSeq data. This is necessary because that machine cannot distinguish between G and reaching the end of the fragment (it encodes G as ‘black’). This option works like regular quality trimming (where one would use -q 20 instead), except that the qualities of G bases are ignored." />
- <param name="trim_n" argument="--trim-n" type="boolean" truevalue="--trim-n" falsevalue="" checked="False" label="Trim Ns" help="Trim N's on ends of reads." />
- <param name="prefix" argument="--prefix" label="Prefix" type="text" help="Add this prefix to read names" />
- <param name="suffix" argument="--suffix" label="Suffix" type="text" help="Add this suffix to read names" />
- <param name="strip_suffix" argument="--strip-suffix" label="Strip suffix" type="text" help="Remove this suffix from read names if present." />
- <param name="length" argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." />
- <param name="length_tag" argument="--length-tag" label="Length Tag" type="text" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." />
+ <param argument="--nextseq-trim" type="integer" value="0" label="NextSeq trimming" help="Experimental option for quality trimming of NextSeq data. This is necessary because that machine cannot distinguish between G and reaching the end of the fragment (it encodes G as ‘black’). This option works like regular quality trimming (where one would use -q 20 instead), except that the qualities of G bases are ignored." />
+ <param argument="--trim-n" type="boolean" truevalue="--trim-n" falsevalue="" checked="False" label="Trim Ns" help="Trim N's on ends of reads." />
+ <param argument="--strip-suffix" label="Strip suffix" type="text" help="Remove this suffix from read names if present." />
+ <param argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." />
+ <param argument="--length-tag" label="Length Tag" type="text" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." />
+ <param argument="--rename" label="Rename reads" type="text" help="This option can be used to rename both single-end and paired-end reads. " />
+ <param argument="--cut" label="Remove a fixed number of bases" type="integer" min="-100" max="100" value="0" help="This option allows to unconditionally remove bases from the beginning or end of each read. If the given length is positive, the bases are removed from the beginning of each read. If it is negative, the bases are removed from the end." />
+ <param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
</section>
<!-- Output Options -->
- <section name="output_options" title="Output Options">
- <param name="report" type="boolean" value="False" label="Report" help="Cutadapt's per-adapter statistics. You can use this file with MultiQC."/>
- <param name="info_file" argument="--info-file" type="boolean" value="False" label="Info File" help="Write information about each read and its adapter matches to a file."/>
- <param name="rest_file" argument="--rest-file" type="boolean" value="False" label="Rest of Read" help="When the adapter matches in the middle of a read, write the rest (after the adapter) into a file."/>
- <param name="wildcard_file" argument="--wildcard-file" type="boolean" value="False" label="Wildcard File" help="When the adapter has wildcard bases ('N's) write adapter bases matching wildcard positions to file."/>
- <param name="too_short_file" argument="--too-short-output" type="boolean" value="False" label="Too Short Reads" help="Write reads that are too short (according to minimum length specified) to a file. (default: discard reads)"/>
- <param name="too_long_file" argument="--too-long-output" type="boolean" value="False" label="Too Long Reads" help="Write reads that are too long (according to maximum length specified) to a file. (default: discard reads)"/>
- <param name="untrimmed_file" argument="--untrimmed-output" type="boolean" value="False" label="Untrimmed Reads" help="Write reads that do not contain the adapter to a separate file, instead of writing them to the regular output file. (default: output to same file as trimmed)"/>
- <param name="multiple_output" argument="" type="boolean" value="False" label="Multiple output" help="Create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)"/>
- </section>
-
+ <param name="output_selector" type="select" multiple="True" display="checkboxes" label="Outputs selector">
+ <option value="report">Report: Cutadapt's per-adapter statistics. You can use this file with MultiQC.</option>
+ <option value="info_file">Info file: write information about each read and its adapter matches.</option>
+ <option value="rest_file">Rest of read: when the adapter matches in the middle of a read, write the rest (after the adapter).</option>
+ <option value="wildcard_file">Wildcard file: when the adapter has wildcard bases (Ns) write adapter bases matching wildcard positions.</option>
+ <option value="too_short_file">Too short reads: write reads that are too short according to minimum length specified (default: discard reads).</option>
+ <option value="too_long_file">Too long reads: write reads that are too long (according to maximum length specified)</option>
+ <option value="untrimmed_file">Untrimmed reads: write reads that do not contain the adapter to a separate file, instead of writing them to the regular output file (default: output to same file as trimmed)</option>
+ <option value="multiple_output">Multiple output: create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)</option>
+ </param>
</inputs>
<outputs>
<data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">
- <filter>(output_options['multiple_output'] is False and library['type'] != 'paired_collection')</filter>
+ <filter>library['type'] != 'paired_collection' and 'multiple_output' not in output_selector</filter>
<expand macro="inherit_format_1" />
</data>
+
<data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" >
- <filter>(output_options['multiple_output'] is False and library['type'] == 'paired')</filter>
+ <filter>library['type'] == 'paired' and 'multiple_output' not in output_selector</filter>
<expand macro="inherit_format_2" />
</data>
<collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads">
- <filter>(output_options['multiple_output'] is False and library['type'] == 'paired_collection')</filter>
+ <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
</collection>
-
+
<data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">
- <filter>(output_options['report'] is True)</filter>
+ <filter>output_selector and 'report' in output_selector</filter>
</data>
-
<data name="info_file" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Info File" >
- <filter>(output_options['info_file'] is True)</filter>
+ <filter>output_selector and 'info_file' in output_selector</filter>
</data>
<data name="rest_output" format="fastqsanger" metadata_source="input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >
- <filter>(output_options['rest_file'] is True)</filter>
+ <filter>output_selector and 'rest_file' in output_selector</filter>
<expand macro="inherit_format_1" />
</data>
<data name="wild_output" format="txt" metadata_source="input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" >
- <filter>(output_options['wildcard_file'] is True)</filter>
+ <filter>output_selector and 'wildcard_file' in output_selector</filter>
</data>
<data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" >
- <filter>(output_options['untrimmed_file'] is True)</filter>
+ <filter>output_selector and 'untrimmed_file' in output_selector</filter>
<expand macro="inherit_format_1" />
</data>
<data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" >
- <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
- <filter>(output_options['untrimmed_file'] is True)</filter>
+ <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
+ <filter>output_selector and 'untrimmed_file' in output_selector </filter>
<expand macro="inherit_format_2" />
</data>
<data name="too_short_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" >
- <filter>(output_options['too_short_file'] is True)</filter>
+ <filter>output_selector and 'too_short_file' in output_selector</filter>
<expand macro="inherit_format_1" />
</data>
<data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" >
- <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
- <filter>(output_options['too_short_file'] is True)</filter>
+ <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
+ <filter>output_selector and 'too_short_file' in output_selector</filter>
<expand macro="inherit_format_2" />
</data>
-
<data name="too_long_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" >
- <filter>(output_options['too_long_file'] is True)</filter>
+ <filter>output_selector and 'too_long_file' in output_selector</filter>
<expand macro="inherit_format_1" />
</data>
<data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >
- <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
- <filter>(output_options['too_long_file'] is True)</filter>
+ <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
+ <filter>output_selector and 'too_long_file' in output_selector</filter>
<expand macro="inherit_format_2" />
</data>
<collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs" >
<discover_datasets pattern="(?P<designation>.+)\.(?P<ext>fastq.*)" directory="split" />
- <filter>(output_options['multiple_output'] is True)</filter>
+ <filter>output_selector and 'multiple_output' in output_selector</filter>
</collection>
-
</outputs>
<tests>
@@ -381,10 +416,9 @@ $read_mod_options.trim_n
<param name="adapter" value="TTAGACATATCTCCGTCG"/>
<param name="output_filtering" value="filter"/>
<section name="filter_options">
- <param name="discard" value="True"/>
+ <param name="discard_trimmed" value="True"/>
</section>
<param name="read_modification" value="none"/>
- <param name="output_type" value="default"/>
<output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
<assert_command>
<has_text text="--discard-trimmed"/>
@@ -397,8 +431,7 @@ $read_mod_options.trim_n
<param name="adapter" value="AAAGATG"/>
<param name="output_filtering" value="default"/>
<param name="read_modification" value="none"/>
- <param name="output_type" value="additional"/>
- <param name="rest_file" value="True"/>
+ <param name="output_selector" value="rest_file"/>
<output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
<output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
</test>
@@ -418,8 +451,7 @@ $read_mod_options.trim_n
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="AGATCGGAAGAGC"/>
- <param name="report" value="True" />
- <param name="info_file" value="True" />
+ <param name="output_selector" value="report,info_file" />
<output name="out1" value="cutadapt_small.out" ftype="fastq"/>
<output name="report">
<assert_contents>
@@ -451,9 +483,7 @@ $read_mod_options.trim_n
</repeat>
</section>
</conditional>
- <param name="report" value="False" />
- <param name="info_file" value="False" />
- <param name="multiple_output" value="True" />
+ <param name="output_selector" value="multiple_output" />
<output_collection name="split_output" type="list" count="3">
<element name="A1" value="A1.fastq" ftype="fastq">
</element>
@@ -477,9 +507,7 @@ $read_mod_options.trim_n
</repeat>
</section>
</conditional>
- <param name="report" value="False" />
- <param name="info_file" value="False" />
- <param name="multiple_output" value="True" />
+ <param name="output_selector" value="multiple_output" />
<output_collection name="split_output" type="list" count="3">
<element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz">
</element>
@@ -496,7 +524,7 @@ $read_mod_options.trim_n
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="AAAT"/>
- <param name="untrimmed_file" value="True" />
+ <param name="output_selector" value="untrimmed_file" />
<output name="out1" file="cutadapt_trimmed.out" ftype="fastq"/>
<output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/>
</test>
@@ -506,7 +534,7 @@ $read_mod_options.trim_n
<param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="AGATCGGAAGAGC"/>
- <param name="untrimmed_file" value="True" />
+ <param name="output_selector" value="untrimmed_file" />
<output name="out1" decompress="True" file="cutadapt_trimmed.out.gz" ftype="fastq.gz"/>
<!--
Do not use the decompress option for this assertion, since it does NOT test that the file is compressed
@@ -534,12 +562,40 @@ $read_mod_options.trim_n
</section>
<assert_command>
<has_text text="--discard-untrimmed"/>
- <has_text text="--minimum-length=1"/>
<has_text text="--maximum-length=1000"/>
<has_text text="--max-n=0"/>
<has_text text="--pair-filter=both"/>
</assert_command>
</test>
+ <!-- Test cut option -->
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="cut" value="5"/>
+ <output name="out1" file="cutadapt_small_cut.out" ftype="fastq"/>
+ </test>
+ <!-- Test rename options -->
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="cut" value="5"/>
+ <param name="rename" value="{prefix:1_13_1259/1} barcode={AGATC} adapter={illumina_adapter}"/>
+ <output name="out1" file="cutadapt_small_rename.out" ftype="fastq"/>
+ </test>
+ <!-- Test rename options -->
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="cut" value="5"/>
+ <param name="rename" value="{prefix:1_13_1259/1} barcode={AGATC} adapter={illumina_adapter}"/>
+ <output name="out1" file="cutadapt_small_rename.out" ftype="fastq"/>
+ </test>
</tests>
<help><![CDATA[
@@ -690,6 +746,30 @@ When parsing the file, be aware that additional columns may be added in the futu
If the --times option is used and greater than 1, each read can appear more than once in the info file. There will be one line for each found adapter, all with identical read names. Only for the first of those lines will the concatenation of columns 5-7 be identical to the original read sequence (and accordingly for columns 9-11). For subsequent lines, the shown sequence are the ones that were used in subsequent rounds of adapter trimming, that is, they get successively shorter.
+
+--------------------
+
+**Rename Reads**
+
+--------------------
+
+
+The --rename option expects a template string such as {id} extra_info {adapter_name} as a parameter. It can contain regular text and placeholders that consist of a name enclosed in curly braces ({placeholdername}).
+
+The read name will be set to the template string in which the placeholders are replaced with the actual values relevant for the current read.
+
+The following placeholders are currently available for single-end reads:
+
+ * {header} – the full, unchanged header
+ * {id} – the read ID, that is, the part of the header before the first whitespace
+ * {comment} – the part of the header after the whitespace following the ID
+ * {adapter_name} – the name of adapter that was found in this read or no_adapter if there was none adapter match. If you use --times to do multiple rounds of adapter matching, this is the name of the last found adapter.
+ * {cut_prefix} – the prefix removed by the --cut (or -u) option (that is, when used with a positive length argument)
+ * {cut_suffix} – the suffix removed by the --cut (or -u) option (that is, when used with a negative length argument)
+
+If the --rename option is used with paired-end data, the template is applied separately to both R1 and R2. That is, for R1, the placeholders are replaced with values from R1, and for R2, the placeholders are replaced with values from R2. For example, {comment} becomes R1’s comment in R1 and it becomes R2’s comment in R2.
+
+
--------------------
**More Information**
@@ -712,27 +792,5 @@ See the excellent `Cutadapt documentation`_
Author: Lance Parsons <lparsons@princeton.edu>
]]></help>
-
- <citations>
- <citation type="bibtex">
-@article{marcel_cutadapt_2011,
- title = {Cutadapt removes adapter sequences from high-throughput sequencing reads},
- volume = {17},
- copyright = {Authors who publish with this journal agree to the following terms: Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access ).},
- url = {http://journal.embnet.org/index.php/embnetjournal/article/view/200},
- abstract = {When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
-
-Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/},
- number = {1},
- urldate = {2011-08-02},
- journal = {EMBnet.journal},
- author = {Marcel, Martin},
- year = {2011},
- note = {When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/},
- keywords = {Adapter removal;, fastq, MicroRNA, Sequencing, Small RNA, software},
- file = {Cutadapt removes adapter sequences from high-throughput sequencing reads | Martin | EMBnet.journal:/Users/lparsons/Library/Application Support/Firefox/Profiles/thd2t4je.default/zotero/storage/ZXZT4PSE/200.html:text/html}
-}
- </citation>
- </citations>
-
+ <expand macro="citations" />
</tool>
diff --git a/tools/cutadapt/macros.xml b/tools/cutadapt/macros.xml
index ef8445bcf5d..9b057d0ecfb 100644
--- a/tools/cutadapt/macros.xml
+++ b/tools/cutadapt/macros.xml
@@ -1,5 +1,29 @@
<macros>
-
+ <token name="@TOOL_VERSION@">3.4</token>
+ <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
+ <xml name="edam_ontology">
+ <edam_topics>
+ <edam_topic>topic_0632</edam_topic>
+ </edam_topics>
+ <edam_operations>
+ <edam_operation>operation_0231</edam_operation>
+ </edam_operations>
+ </xml>
+ <xml name="requirements">
+ <requirements>
+ <requirement type="package" version="@TOOL_VERSION@">cutadapt</requirement>
+ </requirements>
+ </xml>
+ <xml name="citations">
+ <citations>
+ <citation type="doi">10.14806/ej.17.1.200</citation>
+ </citations>
+ </xml>
+ <xml name="xrefs">
+ <xrefs>
+ <xref type='bio.tools'>cutadapt</xref>
+ </xrefs>
+ </xml>
<token name="@read1_options@"><![CDATA[
## Read1 trimming
@@ -44,22 +68,22 @@
## Additional Outputs
- #if $output_options.info_file:
+ #if 'info_file' in $output_selector:
--info-file=$info_file
#end if
- #if $output_options.rest_file:
+ #if 'rest_file' in $output_selector:
--rest-file='${rest_output}'
#end if
- #if $output_options.wildcard_file:
+ #if 'wildcard_file' in $output_selector:
--wildcard-file='${wild_output}'
#end if
- #if $output_options.too_short_file:
+ #if 'too_short_file' in $output_selector:
--too-short-output='${too_short_output}'
#end if
- #if $output_options.too_long_file:
+ #if 'too_long_file' in $output_selector:
--too-long-output='${too_long_output}'
#end if
- #if $output_options.untrimmed_file:
+ #if 'untrimmed_file' in $output_selector:
--untrimmed-output='${untrimmed_output}'
#end if
@@ -109,13 +133,13 @@
## Additional Outputs - Read 2
- #if $output_options.too_short_file:
+ #if 'too_short_file' in $output_selector:
--too-short-paired-output='${too_short_paired_output}'
#end if
- #if $output_options.too_long_file:
+ #if 'too_long_file' in $output_selector:
--too-long-paired-output='${too_long_paired_output}'
#end if
- #if $output_options.untrimmed_file:
+ #if 'untrimmed_file' in $output_selector:
--untrimmed-paired-output='${untrimmed_paired_output}'
#end if
@@ -204,7 +228,7 @@
<param name="front_adapter_source_list" type="select" label="Source">
<option value="builtin" selected="True">Standard (select from the list below)</option>
<option value="user">Enter custom sequence</option>
- <option value="file">File From History</option>
+ <option value="file">File from history</option>
</param>
<when value="user">
@@ -225,7 +249,7 @@
<param name="anywhere_adapter_source_list" type="select" label="Source">
<option value="builtin" selected="True">Standard (select from the list below)</option>
<option value="user">Enter custom sequence</option>
- <option value="file">File From History</option>
+ <option value="file">File from history</option>
</param>
<when value="user">
@@ -260,7 +284,7 @@
<param name="adapter_source_list2" type="select" label="Source" >
<option value="builtin" selected="True">Standard (select from the list below)</option>
<option value="user">Enter custom sequence</option>
- <option value="file">File From History</option>
+ <option value="file">File from history</option>
</param>
<when value="user">
diff --git a/tools/cutadapt/test-data/A1.fastq.gz b/tools/cutadapt/test-data/A1.fastq.gz
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diff --git a/tools/cutadapt/test-data/cutadapt_small_cut.out b/tools/cutadapt/test-data/cutadapt_small_cut.out
new file mode 100644
index 00000000000..383b3dbef37
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_small_cut.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+GAANTAGCTACCACCCTGATTAGACAAAT
++
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+@prefix:1_13_1259/1
+CTANGACGGGTTGGCCCTTAGACGTATCT
++
+A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+TCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+=57!7<';<6?5;;6:+:=)71>70<,=:
diff --git a/tools/cutadapt/test-data/cutadapt_small_rename.out b/tools/cutadapt/test-data/cutadapt_small_rename.out
new file mode 100644
index 00000000000..59c665cdb87
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_small_rename.out
@@ -0,0 +1,12 @@
+@__oc__prefix:1_13_1259/1__cc__ barcode=__oc__AGATC__cc__ adapter=__oc__illumina_adapter__cc__
+GAANTAGCTACCACCCTGATTAGACAAAT
++
+&&&!.1&(6:<'67..*,:75)'77&&&5
+@__oc__prefix:1_13_1259/1__cc__ barcode=__oc__AGATC__cc__ adapter=__oc__illumina_adapter__cc__
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++
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++
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diff --git a/tools/cutadapt/test-data/cutadapt_trimmed.out.gz b/tools/cutadapt/test-data/cutadapt_trimmed.out.gz
index ed6fff795865f01c5dec762cf30e91c70af88e20..f5c8147fdb044e3959b45e42e77db70e70598257 100644
GIT binary patch
delta 17
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delta 17
YcmbQqGLwZvzMF%=v~_vRMh-zH04dJ|egFUf
diff --git a/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz b/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz
index 2ad9b69756051fb36bafdbb9b8eaf50435d4fdc7..abda24d08a27334357d5be7a3d1e2c559e4fa004 100644
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diff --git a/tools/cutadapt/test-data/unknown.fastq.gz b/tools/cutadapt/test-data/unknown.fastq.gz
index 838f7ce4d50cb52ef3b5b5699c7e2893d5ac78d7..77584216601babcf242b1241892ab78ad65bf3a3 100644
GIT binary patch
delta 18
ZcmdnbxR#MizMF%=w_<Ao1M@_g#Q-s_1y}$8
delta 36
rcmZ3>xSvr*zMF%CrBo<}fw?5NAigv&J1@UHPcJR8xTKI_BG+O7!72-S
From 9d469965d9e7513994166025335aabee0308d24e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 02:29:35 +0200
Subject: [PATCH 02/20] Update test minimum maximum length
---
tools/cutadapt/cutadapt.xml | 4 ++--
tools/cutadapt/test-data/A1.fastq.gz | Bin 340 -> 340 bytes
tools/cutadapt/test-data/A2.fastq.gz | Bin 326 -> 326 bytes
.../test-data/cutadapt_nextseq_out.fq.gz | Bin 12158 -> 12158 bytes
.../test-data/cutadapt_trimmed.out.gz | Bin 537 -> 537 bytes
.../test-data/cutadapt_untrimmed.out.gz | Bin 12095 -> 12095 bytes
tools/cutadapt/test-data/unknown.fastq.gz | Bin 173 -> 173 bytes
7 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 1fb98d550b6..628607ed3c5 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -555,8 +555,8 @@ $read_mod_options.zero_cap
<param name="adapter2" value="AGATCGGAAGAGC"/>
<section name="filter_options">
<param name="discard_untrimmed" value="true"/>
- <param name="min" value="1"/>
- <param name="max" value="1000"/>
+ <param name="minimun_length" value="1"/>
+ <param name="maximum_length" value="1000"/>
<param name="max_n" value="0"/>
<param name="pair_filter" value="both"/>
</section>
diff --git a/tools/cutadapt/test-data/A1.fastq.gz b/tools/cutadapt/test-data/A1.fastq.gz
index a320d511b969d75b05cc7450dbb30ac2c75bc29c..5cb14c45dad458afedee2dddf5931087f23d9ee7 100644
GIT binary patch
delta 15
Wcmcb@bcKmczMF$Vwq_%nA0q%Hn*;;^
delta 15
Wcmcb@bcKmczMF%=w_+okA0q%Irvxwn
diff --git a/tools/cutadapt/test-data/A2.fastq.gz b/tools/cutadapt/test-data/A2.fastq.gz
index 1347273c15fe03862ec60ad5cadbf15f70635266..d6c4b5006d0ab868313e1a98a56dfca458bfd957 100644
GIT binary patch
delta 15
WcmX@cbc~5jzMF$Vwq_%n10w(;_XFAh
delta 15
WcmX@cbc~5jzMF%=w_+ok10w(=0|W*D
diff --git a/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz b/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz
index fdbe9f3688e2787c67f24d29cd11e943d9e901dc..9e773cbc88c0eb29196ae46b305ef2b6080d332b 100644
GIT binary patch
delta 15
Wcmewt_b-l3zMF&LUiC({3Vi@Kjs_?I
delta 15
Wcmewt_b-l3zMF%Aw_+n(g+2f>nFUk;
diff --git a/tools/cutadapt/test-data/cutadapt_trimmed.out.gz b/tools/cutadapt/test-data/cutadapt_trimmed.out.gz
index f5c8147fdb044e3959b45e42e77db70e70598257..a03b905a25c5081254b98a4be9cd5f7f5884e9c7 100644
GIT binary patch
delta 15
WcmbQqGLwZ(zMF%=yJjPsFcSbC`U8dl
delta 15
WcmbQqGLwZ(zMF%gvSK5fFcSbD`U9{4
diff --git a/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz b/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz
index abda24d08a27334357d5be7a3d1e2c559e4fa004..e07fdd2f3d491369f6b01219d147654a2a03849f 100644
GIT binary patch
delta 15
WcmdlVw?B?ezMF%=yJjPsr9J>GzXaI;
delta 15
WcmdlVw?B?ezMF%gvSK5fr9J>HzXbyT
diff --git a/tools/cutadapt/test-data/unknown.fastq.gz b/tools/cutadapt/test-data/unknown.fastq.gz
index 77584216601babcf242b1241892ab78ad65bf3a3..bf1313d639a536c1bccb5b17c4d35ece8c138f34 100644
GIT binary patch
delta 14
VcmZ3>xR#MkzMF$Vwq_#RasV8H1MC0*
delta 14
VcmZ3>xR#MkzMF%=w_+mOasVA-1Q-AS
From f9875ae94521275ea3ba323937563c847a3599a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 02:30:50 +0200
Subject: [PATCH 03/20] Increase default cores
---
tools/cutadapt/cutadapt.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 628607ed3c5..9d0db37eeb1 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -77,7 +77,7 @@ ln -f -s '${input_1}' '$read1' &&
cutadapt
--j=\${GALAXY_SLOTS:-1}
+-j=\${GALAXY_SLOTS:-4}
#if str( $library.type ) == "single":
@read1_options@
From 841f1405e72f920bda5851bafd6179ff383e19eb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 16:30:52 +0200
Subject: [PATCH 04/20] Update tests
---
tools/cutadapt/cutadapt.xml | 165 ++++++++++++++----
tools/cutadapt/test-data/A1.fastq.gz | Bin 340 -> 340 bytes
tools/cutadapt/test-data/A2.fastq.gz | Bin 326 -> 326 bytes
.../test-data/bwa-mem-fastq1_assimetric.fq.gz | Bin 0 -> 11764 bytes
.../test-data/bwa-mem-fastq2_assimetric.fq.gz | Bin 0 -> 11747 bytes
.../test-data/cutadapt_action_lowercase.out | 12 ++
.../test-data/cutadapt_action_mask.out | 12 ++
.../test-data/cutadapt_action_none.out | 12 ++
.../test-data/cutadapt_action_retain.out | 12 ++
.../test-data/cutadapt_nextseq_out.fq.gz | Bin 12158 -> 12158 bytes
tools/cutadapt/test-data/cutadapt_revcomp.out | 12 ++
.../test-data/cutadapt_trimmed.out.gz | Bin 537 -> 537 bytes
.../test-data/cutadapt_untrimmed.out.gz | Bin 12095 -> 12095 bytes
tools/cutadapt/test-data/unknown.fastq.gz | Bin 173 -> 173 bytes
14 files changed, 194 insertions(+), 31 deletions(-)
create mode 100644 tools/cutadapt/test-data/bwa-mem-fastq1_assimetric.fq.gz
create mode 100644 tools/cutadapt/test-data/bwa-mem-fastq2_assimetric.fq.gz
create mode 100644 tools/cutadapt/test-data/cutadapt_action_lowercase.out
create mode 100644 tools/cutadapt/test-data/cutadapt_action_mask.out
create mode 100644 tools/cutadapt/test-data/cutadapt_action_none.out
create mode 100644 tools/cutadapt/test-data/cutadapt_action_retain.out
create mode 100644 tools/cutadapt/test-data/cutadapt_revcomp.out
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 9d0db37eeb1..61acf3e7e13 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -109,12 +109,12 @@ $adapter_options.revcomp
$filter_options.discard_trimmed
$filter_options.discard_untrimmed
-#if str($filter_options.minimum_options.minimum_r2):
+#if str($filter_options.minimum_options.minimum_r2) == 'true':
--minimum-length=$filter_options.minimum_length:$filter_options.minimum_options.value_minimum
#elif str($filter_options.minimum_length)
--minimum-length=$filter_options.minimum_length
#end if
-#if str($filter_options.maximum_options.maximum_r2):
+#if str($filter_options.maximum_options.maximum_r2) == 'true':
--maximum-length=$filter_options.maximum_length:$filter_options.maximum_options.value_maximum
#elif str($filter_options.maximum_length)
--maximum-length=$filter_options.maximum_length
@@ -196,7 +196,7 @@ $read_mod_options.zero_cap
<param name="action" type="select" label="What to do if a match is found">
<option value="trim" selected="True">Trim: trim adapter and upstream or downstream sequence</option>
<option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option>
- <option value="mask">Mask: madapters with 'N' characters instead of trimming them</option>
+ <option value="mask">Mask: mask adapters with 'N' characters instead of trimming them</option>
<option value="lowercase">Lowercase: convert to lowercase</option>
<option value="none">None: leave unchanged</option>
</param>
@@ -221,30 +221,32 @@ $read_mod_options.zero_cap
<conditional name="minimum_options">
<param name="minimum_r2" type="select" label="Specify a minimum length for reverse reads (R2)" help="When trimming paired-end reads, the minimum lengths for R1 and R2 can be specified separately. If not provided, the same minimum length applies to both reads.">
<option value="true">Enable</option>
- <option value="" selected="True">Disable</option>
+ <option value="false" selected="True">Disable</option>
</param>
<when value="true">
<param name="value_minimum" type="integer" min="0" optional="True" value="" label="Minimum length" />
</when>
- <when value="">
+ <when value="false">
</when>
</conditional>
<param argument="--maximum-length" type="integer" min="0" optional="True" value="" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
<conditional name="maximum_options">
<param name="maximum_r2" type="select" label="Specify a maximum length for reverse reads (R2)" help="When trimming paired-end reads, the maximum lengths for R1 and R2 can be specified separately. If not provided, the same maximum length applies to both reads.">
<option value="true">Enable</option>
- <option value="" selected="True">Disable</option>
+ <option value="false" selected="True">Disable</option>
</param>
<when value="true">
<param name="value_maximum" type="integer" min="0" optional="True" value="" label="Maximum length" />
</when>
- <when value="">
+ <when value="false">
</when>
</conditional>
<param argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
<param argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
- <option value="any" selected="True">any</option>
- <option value="both">both</option>
+ <option value="any" selected="True">Any: a read pair is discarded (or redirected) if one of the reads (R1 or R2) fulfills the filtering criterion. </option>
+ <option value="both">Both: filtering criteria must apply to both reads in order for a read pair to be discarded. </option>
+ <option value="first">First: will make a decision about the read pair by inspecting whether the filtering criterion applies to the first read, ignoring the second read.</option>
+
</param>
<param argument="--max-expected-errors" type="integer" min="0" optional="True" value="" label="Max expected errors" help="Discard reads whose expected number of errors (computed from quality values) exceeds this value." />
<param argument="--discard-cassava" type="boolean" truevalue="--discard-cassava" falsevalue="" checked="False" label="Discard CASAVA filtering" help="Discard reads that did not pass CASAVA filtering (header has :Y:)." />
@@ -586,15 +588,111 @@ $read_mod_options.zero_cap
<param name="rename" value="{prefix:1_13_1259/1} barcode={AGATC} adapter={illumina_adapter}"/>
<output name="out1" file="cutadapt_small_rename.out" ftype="fastq"/>
</test>
- <!-- Test rename options -->
+ <!-- Test action options -->
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="CGTCCGAANTAG"/>
+ <param name="action" value="retain"/>
+ <output name="out1" file="cutadapt_action_retain.out" ftype="fastq"/>
+ </test>
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="CGTCCGAANTAG"/>
+ <param name="action" value="mask"/>
+ <output name="out1" file="cutadapt_action_mask.out" ftype="fastq"/>
+ </test>
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="CGTCCGAANTAG"/>
+ <param name="action" value="lowercase"/>
+ <output name="out1" file="cutadapt_action_lowercase.out" ftype="fastq"/>
+ </test>
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="CGTCCGAANTAG"/>
+ <param name="action" value="none"/>
+ <output name="out1" file="cutadapt_action_none.out" ftype="fastq"/>
+ </test>
+ <!-- Test revcomp options -->
<test expect_num_outputs="1">
<param name="type" value="single" />
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="TAAACAGATTAGT"/>
+ <param name="revcomp" value="true"/>
+ <output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/>
+ </test>
+ <!-- Test minimum lenghth paired-reads -->
+ <test expect_num_outputs="2">
+ <param name="type" value="paired" />
+ <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
+ <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
+ <param name="adapter_source_list" value="user"/>
<param name="adapter" value="AGATCGGAAGAGC"/>
- <param name="cut" value="5"/>
- <param name="rename" value="{prefix:1_13_1259/1} barcode={AGATC} adapter={illumina_adapter}"/>
- <output name="out1" file="cutadapt_small_rename.out" ftype="fastq"/>
+ <param name="adapter_source_list2" value="user"/>
+ <param name="adapter2" value="AGATCGGAAGAGC"/>
+ <section name="filter_options">
+ <param name="minimun_length" value="30"/>
+ <param name="pair_filter" value="both"/>
+ <conditional name="minimum_option">
+ <param name="minimum_r2" value="true"/>
+ <param name="value_minimum" value="10"/>
+ </conditional>
+ </section>
+ <output name="out1" ftype="fastq.gz">
+ <assert_contents>
+ <has_size value="12180"/>
+ </assert_contents>
+ </output>
+ <output name="out2" ftype="fastq.gz">
+ <assert_contents>
+ <has_size value="12153"/>
+ </assert_contents>
+ </output>
+ <assert_command>
+ <has_text text="--minimum-length=30:10"/>
+ <has_text text="--pair-filter=both"/>
+ </assert_command>
+ </test>
+ <!-- Test maximum lenghth paired-reads -->
+ <test expect_num_outputs="2">
+ <param name="type" value="paired" />
+ <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
+ <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="adapter_source_list2" value="user"/>
+ <param name="adapter2" value="AGATCGGAAGAGC"/>
+ <section name="filter_options">
+ <param name="pair_filter" value="both"/>
+ <param name="maximum_length" value="50"/>
+ <conditional name="maximum_option">
+ <param name="maximum_r2" value="true"/>
+ <param name="value_maximum" value="30"/>
+ </conditional>
+ </section>
+ <output name="out1" ftype="fastq.gz">
+ <assert_contents>
+ <has_size value="134"/>
+ </assert_contents>
+ </output>
+ <output name="out2" ftype="fastq.gz">
+ <assert_contents>
+ <has_size value="139"/>
+ </assert_contents>
+ </output>
+ <assert_command>
+ <has_text text="--maximum-length=50:30"/>
+ <has_text text="--pair-filter=both"/>
+ </assert_command>
</test>
</tests>
@@ -694,25 +792,30 @@ Cutadapt can output per-adapter statistics if you select to output the report ab
Example:
- *This is cutadapt 1.16 with Python 3.6.4*
-
- *Command line parameters: -j 1 --format=fastq -a AGATCGGAAGAGC --info-file=/tmp/tmpX0DlY1/files/000/dataset_21.dat --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 input_f.fastq*
- *Running on 1 core*
- *Trimming 1 adapter with at most 10.0% errors in single-end mode ...*
- *Finished in 0.00 s (1426 us/read; 0.04 M reads/minute).*
-
- *=== Summary ===*
-
- * Total reads processed: 3*
- * Reads with adapters: 0 (0.0%)*
- * Reads written (passing filters): 3 (100.0%)*
-
- * Total basepairs processed: 102 bp*
- * Total written (filtered): 102 bp (100.0%)*
-
- *=== Adapter 1 ===*
+ ::
+
+ This is cutadapt 3.4 with Python 3.9.2
- *Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times.*
+ Command line parameters: -j=1 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1
+ --overlap=3 --action=trim --minimum-length=30:40 --pair-filter=both --cut=0 bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz
+
+ Processing reads on 1 core in paired-end mode ...
+ Finished in 0.01 s (129 µs/read; 0.46 M reads/minute).
+
+ === Summary ===
+
+ Total read pairs processed: 99
+ Read 1 with adapter: 2 (2.0%)
+ Read 2 with adapter: 4 (4.0%)
+ Pairs that were too short: 3 (3.0%)
+ Pairs written (passing filters): 96 (97.0%)
+
+ Total basepairs processed: 48,291 bp
+ Read 1: 24,147 bp
+ Read 2: 24,144 bp
+ Total written (filtered): 48,171 bp (99.8%)
+ Read 1: 24,090 bp
+ Read 2: 24,081 bp
**Info file**
diff --git a/tools/cutadapt/test-data/A1.fastq.gz b/tools/cutadapt/test-data/A1.fastq.gz
index 5cb14c45dad458afedee2dddf5931087f23d9ee7..e8c0e369417c5b11dc18023839d11b8f0488fa13 100644
GIT binary patch
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diff --git a/tools/cutadapt/test-data/A2.fastq.gz b/tools/cutadapt/test-data/A2.fastq.gz
index d6c4b5006d0ab868313e1a98a56dfca458bfd957..87222d183c4ddd81e6ddaba2f6fb2bbfbc62b01e 100644
GIT binary patch
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diff --git a/tools/cutadapt/test-data/bwa-mem-fastq1_assimetric.fq.gz b/tools/cutadapt/test-data/bwa-mem-fastq1_assimetric.fq.gz
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F008rg<c0tM
literal 0
HcmV?d00001
diff --git a/tools/cutadapt/test-data/cutadapt_action_lowercase.out b/tools/cutadapt/test-data/cutadapt_action_lowercase.out
new file mode 100644
index 00000000000..767ca2279af
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_action_lowercase.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:
diff --git a/tools/cutadapt/test-data/cutadapt_action_mask.out b/tools/cutadapt/test-data/cutadapt_action_mask.out
new file mode 100644
index 00000000000..767ca2279af
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_action_mask.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:
diff --git a/tools/cutadapt/test-data/cutadapt_action_none.out b/tools/cutadapt/test-data/cutadapt_action_none.out
new file mode 100644
index 00000000000..767ca2279af
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_action_none.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
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+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
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+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
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diff --git a/tools/cutadapt/test-data/cutadapt_action_retain.out b/tools/cutadapt/test-data/cutadapt_action_retain.out
new file mode 100644
index 00000000000..767ca2279af
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_action_retain.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
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+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:
diff --git a/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz b/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz
index 9e773cbc88c0eb29196ae46b305ef2b6080d332b..a5cc399b1d1a68a7c806213aa8d91f72032f9b53 100644
GIT binary patch
delta 16
Xcmewt_b-lJzMF%g+j`qZ_HumyJT3-I
delta 16
Xcmewt_b-lJzMF&LUiH?E?B)6ZKkf$J
diff --git a/tools/cutadapt/test-data/cutadapt_revcomp.out b/tools/cutadapt/test-data/cutadapt_revcomp.out
new file mode 100644
index 00000000000..78889906185
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_revcomp.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGT
++
+<=A:A=57!7<';<6?5;;6:+:=)71>7
diff --git a/tools/cutadapt/test-data/cutadapt_trimmed.out.gz b/tools/cutadapt/test-data/cutadapt_trimmed.out.gz
index a03b905a25c5081254b98a4be9cd5f7f5884e9c7..a3dc7d22690c1d3067a07df0a4606640d277f350 100644
GIT binary patch
delta 16
XcmbQqGLwZ}zMF&LyY;q>>_SWcD18K|
delta 16
XcmbQqGLwZ}zMF%=yJqV~b|EGJB}xQ5
diff --git a/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz b/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz
index e07fdd2f3d491369f6b01219d147654a2a03849f..ea8a361655da60e2a8a62851b0537c80b6c697f5 100644
GIT binary patch
delta 16
XcmdlVw?B?uzMF&LyY;q>>=ya}H$nyb
delta 16
XcmdlVw?B?uzMF%=yJqV~b_;y~G!F%j
diff --git a/tools/cutadapt/test-data/unknown.fastq.gz b/tools/cutadapt/test-data/unknown.fastq.gz
index bf1313d639a536c1bccb5b17c4d35ece8c138f34..8f72df89453d2ee619707d46812c5f7595e6b2ba 100644
GIT binary patch
delta 15
WcmZ3>xR#M!zMF&Lr1iFm?8^Wo*98s$
delta 15
WcmZ3>xR#M!zMF$Vwr1-@_GJJf5CozC
From 838f0817c6de701b4c19ee76ff63619a1f9a729c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 16:55:40 +0200
Subject: [PATCH 05/20] Update tests max and min length
---
tools/cutadapt/cutadapt.xml | 28 ++++--------------
tools/cutadapt/test-data/A1.fastq.gz | Bin 340 -> 340 bytes
tools/cutadapt/test-data/A2.fastq.gz | Bin 326 -> 326 bytes
.../test-data/cutadapt_action_lowercase.out | 2 +-
.../test-data/cutadapt_action_mask.out | 2 +-
.../test-data/cutadapt_action_retain.out | 4 +--
.../test-data/cutadapt_nextseq_out.fq.gz | Bin 12158 -> 12158 bytes
.../test-data/cutadapt_out1_max_length.fq.gz | Bin 0 -> 134 bytes
.../test-data/cutadapt_out1_min_length.fq.gz | Bin 0 -> 12155 bytes
.../test-data/cutadapt_out2_max_length.fq.gz | Bin 0 -> 139 bytes
.../test-data/cutadapt_out2_min_length.fq.gz | Bin 0 -> 12138 bytes
.../test-data/cutadapt_trimmed.out.gz | Bin 537 -> 537 bytes
.../test-data/cutadapt_untrimmed.out.gz | Bin 12095 -> 12095 bytes
tools/cutadapt/test-data/unknown.fastq.gz | Bin 173 -> 173 bytes
14 files changed, 10 insertions(+), 26 deletions(-)
create mode 100644 tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz
create mode 100644 tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz
create mode 100644 tools/cutadapt/test-data/cutadapt_out2_max_length.fq.gz
create mode 100644 tools/cutadapt/test-data/cutadapt_out2_min_length.fq.gz
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 61acf3e7e13..fe88415053c 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -642,21 +642,13 @@ $read_mod_options.zero_cap
<section name="filter_options">
<param name="minimun_length" value="30"/>
<param name="pair_filter" value="both"/>
- <conditional name="minimum_option">
+ <conditional name="minimum_options">
<param name="minimum_r2" value="true"/>
<param name="value_minimum" value="10"/>
</conditional>
</section>
- <output name="out1" ftype="fastq.gz">
- <assert_contents>
- <has_size value="12180"/>
- </assert_contents>
- </output>
- <output name="out2" ftype="fastq.gz">
- <assert_contents>
- <has_size value="12153"/>
- </assert_contents>
- </output>
+ <output name="out1" decompress="True" file="cutadapt_out1_min_length.fq.gz" ftype="fastq.gz"/>
+ <output name="out2" decompress="True" file="cutadapt_out2_min_length.fq.gz" ftype="fastq.gz"/>
<assert_command>
<has_text text="--minimum-length=30:10"/>
<has_text text="--pair-filter=both"/>
@@ -674,21 +666,13 @@ $read_mod_options.zero_cap
<section name="filter_options">
<param name="pair_filter" value="both"/>
<param name="maximum_length" value="50"/>
- <conditional name="maximum_option">
+ <conditional name="maximum_options">
<param name="maximum_r2" value="true"/>
<param name="value_maximum" value="30"/>
</conditional>
</section>
- <output name="out1" ftype="fastq.gz">
- <assert_contents>
- <has_size value="134"/>
- </assert_contents>
- </output>
- <output name="out2" ftype="fastq.gz">
- <assert_contents>
- <has_size value="139"/>
- </assert_contents>
- </output>
+ <output name="out1" decompress="True" file="cutadapt_out1_max_length.fq.gz" ftype="fastq.gz"/>
+ <output name="out2" decompress="True" file="cutadapt_out2_max_length.fq.gz" ftype="fastq.gz"/>
<assert_command>
<has_text text="--maximum-length=50:30"/>
<has_text text="--pair-filter=both"/>
diff --git a/tools/cutadapt/test-data/A1.fastq.gz b/tools/cutadapt/test-data/A1.fastq.gz
index e8c0e369417c5b11dc18023839d11b8f0488fa13..1635e3cc999c2a60c131ac85df585770c8fa803d 100644
GIT binary patch
delta 15
Wcmcb@bcKmczMF%=#BC#+A0q%H7X#%0
delta 15
Wcmcb@bcKmczMF&Lr1eHNKSls2UIcFd
diff --git a/tools/cutadapt/test-data/A2.fastq.gz b/tools/cutadapt/test-data/A2.fastq.gz
index 87222d183c4ddd81e6ddaba2f6fb2bbfbc62b01e..4e4bb5ce630e4718f5c87e20e692c25b5d8892e3 100644
GIT binary patch
delta 15
WcmX@cbc~5jzMF%=#BC#+10w(;a|62o
delta 15
WcmX@cbc~5jzMF&Lr1eHN2SxxTx&%c4
diff --git a/tools/cutadapt/test-data/cutadapt_action_lowercase.out b/tools/cutadapt/test-data/cutadapt_action_lowercase.out
index 767ca2279af..927187c4252 100644
--- a/tools/cutadapt/test-data/cutadapt_action_lowercase.out
+++ b/tools/cutadapt/test-data/cutadapt_action_lowercase.out
@@ -1,5 +1,5 @@
@prefix:1_13_573/1
-CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
+cgtccgaantagctaccaccctgattagacaaat
+
)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
@prefix:1_13_1259/1
diff --git a/tools/cutadapt/test-data/cutadapt_action_mask.out b/tools/cutadapt/test-data/cutadapt_action_mask.out
index 767ca2279af..4a74f4fc477 100644
--- a/tools/cutadapt/test-data/cutadapt_action_mask.out
+++ b/tools/cutadapt/test-data/cutadapt_action_mask.out
@@ -1,5 +1,5 @@
@prefix:1_13_573/1
-CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
@prefix:1_13_1259/1
diff --git a/tools/cutadapt/test-data/cutadapt_action_retain.out b/tools/cutadapt/test-data/cutadapt_action_retain.out
index 767ca2279af..63a354ebefe 100644
--- a/tools/cutadapt/test-data/cutadapt_action_retain.out
+++ b/tools/cutadapt/test-data/cutadapt_action_retain.out
@@ -1,7 +1,7 @@
@prefix:1_13_573/1
-CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
+CGTCCGAANTAG
+
-)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+)3%)&&&&!.1&
@prefix:1_13_1259/1
AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
+
diff --git a/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz b/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz
index a5cc399b1d1a68a7c806213aa8d91f72032f9b53..80c3d43467770d941abfbf95029ab645efcbf5d4 100644
GIT binary patch
delta 15
Wcmewt_b-l3zMF&Li|a<V3Vi@K1O^BI
delta 15
Wcmewt_b-l3zMF%g+j=8gg+2f@Tm_W?
diff --git a/tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..16ee3977765cee609b89cbd42d0a2cc529c51f27
GIT binary patch
literal 134
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literal 0
HcmV?d00001
diff --git a/tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..d2b182f3b1876854bdb58d04512afff6988b59ef
GIT binary patch
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literal 0
HcmV?d00001
diff --git a/tools/cutadapt/test-data/cutadapt_trimmed.out.gz b/tools/cutadapt/test-data/cutadapt_trimmed.out.gz
index a3dc7d22690c1d3067a07df0a4606640d277f350..5adaf22b4068071be4ac95d0fb38fbfba90a0c6f 100644
GIT binary patch
delta 15
WcmbQqGLwZ(zMF#~(QPA}FcSbCa06xl
delta 15
WcmbQqGLwZ(zMF&LyY)skVI}|}y#w(8
diff --git a/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz b/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz
index ea8a361655da60e2a8a62851b0537c80b6c697f5..6b9e56db4e06c688287bfdc6fca4151e87173fea 100644
GIT binary patch
delta 15
WcmdlVw?B?ezMF#~(QPA}r9J>GH3Yc;
delta 15
WcmdlVw?B?ezMF&LyY)skOML(@f(1kX
diff --git a/tools/cutadapt/test-data/unknown.fastq.gz b/tools/cutadapt/test-data/unknown.fastq.gz
index 8f72df89453d2ee619707d46812c5f7595e6b2ba..13b4154300f7aaa2371c3eb1d1254d55ab0d0ba2 100644
GIT binary patch
delta 14
VcmZ3>xR#MkzMF%=#BCzmasV711I+*c
delta 14
VcmZ3>xR#MkzMF&Lr1eC$<p3Vq1Xln6
From 8927ff7e590c7930ce9866ddceef49cdfd3e3e86 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 17:00:15 +0200
Subject: [PATCH 06/20] Fix typo
---
tools/cutadapt/cutadapt.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index fe88415053c..b14dbd31a77 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -640,7 +640,7 @@ $read_mod_options.zero_cap
<param name="adapter_source_list2" value="user"/>
<param name="adapter2" value="AGATCGGAAGAGC"/>
<section name="filter_options">
- <param name="minimun_length" value="30"/>
+ <param name="minimum_length" value="30"/>
<param name="pair_filter" value="both"/>
<conditional name="minimum_options">
<param name="minimum_r2" value="true"/>
From a364f88c52f51a9e80340c1ebae6c53151fb35f4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 21:49:36 +0200
Subject: [PATCH 07/20] Update tests
---
tools/cutadapt/cutadapt.xml | 180 ++++++++++++++----
tools/cutadapt/macros.xml | 38 ++--
tools/cutadapt/test-data/A1.fastq.gz | Bin 340 -> 340 bytes
tools/cutadapt/test-data/A2.fastq.gz | Bin 326 -> 326 bytes
.../test-data/cutadapt_nextseq_out.fq.gz | Bin 12158 -> 12158 bytes
.../cutadapt_out1_internal_adapter.fq.gz | Bin 0 -> 12180 bytes
.../test-data/cutadapt_out1_max_length.fq.gz | Bin 134 -> 134 bytes
.../test-data/cutadapt_out1_min_length.fq.gz | Bin 12155 -> 9298 bytes
.../cutadapt_out2_internal_adapter.fq.gz | Bin 0 -> 12153 bytes
.../test-data/cutadapt_out2_max_length.fq.gz | Bin 139 -> 139 bytes
.../test-data/cutadapt_out2_min_length.fq.gz | Bin 12138 -> 10480 bytes
.../test-data/cutadapt_shorten_3prime.out | 12 ++
.../test-data/cutadapt_shorten_5prime.out | 12 ++
.../cutadapt_shorten_expected_errors.out | 12 ++
.../cutadapt_shorten_internal_adapters.out | 12 ++
.../test-data/cutadapt_trimmed.out.gz | Bin 537 -> 537 bytes
.../test-data/cutadapt_untrimmed.out.gz | Bin 12095 -> 12095 bytes
tools/cutadapt/test-data/unknown.fastq.gz | Bin 173 -> 173 bytes
18 files changed, 211 insertions(+), 55 deletions(-)
create mode 100644 tools/cutadapt/test-data/cutadapt_out1_internal_adapter.fq.gz
create mode 100644 tools/cutadapt/test-data/cutadapt_out2_internal_adapter.fq.gz
create mode 100644 tools/cutadapt/test-data/cutadapt_shorten_3prime.out
create mode 100644 tools/cutadapt/test-data/cutadapt_shorten_5prime.out
create mode 100644 tools/cutadapt/test-data/cutadapt_shorten_expected_errors.out
create mode 100644 tools/cutadapt/test-data/cutadapt_shorten_internal_adapters.out
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index b14dbd31a77..300970a96a8 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -109,14 +109,14 @@ $adapter_options.revcomp
$filter_options.discard_trimmed
$filter_options.discard_untrimmed
-#if str($filter_options.minimum_options.minimum_r2) == 'true':
+#if str($filter_options.minimum_options.minimum_r2) == 'True':
--minimum-length=$filter_options.minimum_length:$filter_options.minimum_options.value_minimum
-#elif str($filter_options.minimum_length)
+#elif str($filter_options.minimum_length):
--minimum-length=$filter_options.minimum_length
#end if
-#if str($filter_options.maximum_options.maximum_r2) == 'true':
+#if str($filter_options.maximum_options.maximum_r2) == 'True':
--maximum-length=$filter_options.maximum_length:$filter_options.maximum_options.value_maximum
-#elif str($filter_options.maximum_length)
+#elif str($filter_options.maximum_length):
--maximum-length=$filter_options.maximum_length
#end if
#if str($filter_options.max_n):
@@ -139,16 +139,20 @@ $filter_options.discard_untrimmed
--nextseq-trim=$read_mod_options.nextseq_trim
#end if
$read_mod_options.trim_n
-#if str($read_mod_options.length) != '0':
- --length=$read_mod_options.length
+#if str($read_mod_options.shorten_options.shorten_values) == 'True':
+ #if str($read_mod_options.shorten_options.shorten_end) == '3prime'
+ --length=$read_mod_options.shorten_options.length
+ #else
+ --length=-$read_mod_options.shorten_options.length
+ #end if
#end if
-#if $read_mod_options.length_tag != '':
+#if str($read_mod_options.length_tag) != '':
--length-tag='$read_mod_options.length_tag'
#end if
-#if $read_mod_options.cut != '0':
+#if str($read_mod_options.cut) != '0':
--cut=$read_mod_options.cut
#end if
-#if $read_mod_options.rename != '':
+#if str($read_mod_options.rename) != '':
--rename='$read_mod_options.rename'
#end if
$read_mod_options.zero_cap
@@ -200,17 +204,20 @@ $read_mod_options.zero_cap
<option value="lowercase">Lowercase: convert to lowercase</option>
<option value="none">None: leave unchanged</option>
</param>
+ <param name="internal" type="select" label="Disallow internal adaptor ocurrences" help="TODO">
+ <option value="X">Enabled</option>
+ <option value="" selected="True">Disabled</option>
+ </param>
<param argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
<param argument="--no-indels" type="boolean" value="False" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
<param argument="--times" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
<param argument="--overlap" type="integer" min="1" value="3" label="Minimum overlap length" help="Minimum overlap length. If the overlap between the adapter and the sequence is shorter than LENGTH, the read is not modified. This reduces the number of bases trimmed purely due to short random adapter matches." />
- <param name="match_read_wildcards" type="select" label="Match Wildcards" help="Allow 'N's as matches. Default: In the adapters but not in the reads">
+ <param name="match_read_wildcards" type="select" label="Match wildcards" help="Allow 'N's as matches. Default: in the adapters but not in the reads">
<option value=" " selected="True">In the adapters but not in the reads</option>
<option value="--match-read-wildcards">In the adapters and in the reads</option>
<option value="--no-match-adapter-wildcards">Nowhere</option>
</param>
<param argument="--revcomp" type="boolean" value="False" truevalue="--revcomp" falsevalue="" label="Look for adapters in the reverse complement" help="Check both the read and its reverse complement for adapter matches. If match is on reverse-complemented version, output that one. Default: check only read." />
-
</section>
<!-- Filter Options -->
@@ -220,25 +227,25 @@ $read_mod_options.zero_cap
<param argument="--minimum-length" type="integer" min="0" optional="True" value="" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
<conditional name="minimum_options">
<param name="minimum_r2" type="select" label="Specify a minimum length for reverse reads (R2)" help="When trimming paired-end reads, the minimum lengths for R1 and R2 can be specified separately. If not provided, the same minimum length applies to both reads.">
- <option value="true">Enable</option>
- <option value="false" selected="True">Disable</option>
+ <option value="True">Enabled</option>
+ <option value="False" selected="True">Disabled</option>
</param>
- <when value="true">
+ <when value="True">
<param name="value_minimum" type="integer" min="0" optional="True" value="" label="Minimum length" />
</when>
- <when value="false">
+ <when value="False">
</when>
</conditional>
<param argument="--maximum-length" type="integer" min="0" optional="True" value="" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
<conditional name="maximum_options">
<param name="maximum_r2" type="select" label="Specify a maximum length for reverse reads (R2)" help="When trimming paired-end reads, the maximum lengths for R1 and R2 can be specified separately. If not provided, the same maximum length applies to both reads.">
- <option value="true">Enable</option>
- <option value="false" selected="True">Disable</option>
+ <option value="True">Enabled</option>
+ <option value="False" selected="True">Disabled</option>
</param>
- <when value="true">
+ <when value="True">
<param name="value_maximum" type="integer" min="0" optional="True" value="" label="Maximum length" />
</when>
- <when value="false">
+ <when value="False">
</when>
</conditional>
<param argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
@@ -262,9 +269,25 @@ $read_mod_options.zero_cap
<param argument="--nextseq-trim" type="integer" value="0" label="NextSeq trimming" help="Experimental option for quality trimming of NextSeq data. This is necessary because that machine cannot distinguish between G and reaching the end of the fragment (it encodes G as ‘black’). This option works like regular quality trimming (where one would use -q 20 instead), except that the qualities of G bases are ignored." />
<param argument="--trim-n" type="boolean" truevalue="--trim-n" falsevalue="" checked="False" label="Trim Ns" help="Trim N's on ends of reads." />
<param argument="--strip-suffix" label="Strip suffix" type="text" help="Remove this suffix from read names if present." />
- <param argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." />
+ <conditional name="shorten_options">
+ <param name="shorten_values" type="select" label="Shortening reads to a fixed length" help="If you want to remove a fixed number of bases from each read, use the –cut option instead.">
+ <option value="True">Enabled</option>
+ <option value="False" selected="True">Disabled</option>
+ </param>
+ <when value="True">
+ <param argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." />
+ <param name="shorten_end" type="select" label="End at which to apply the slice">
+ <option value="3prime">3' ends</option>
+ <option value="5prime">5' ends</option>
+ </param>
+ </when>
+ <when value="False">
+ </when>
+ </conditional>
<param argument="--length-tag" label="Length Tag" type="text" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." />
- <param argument="--rename" label="Rename reads" type="text" help="This option can be used to rename both single-end and paired-end reads. " />
+ <param argument="--rename" label="Rename reads" type="text" optional="True" help="This option can be used to rename both single-end and paired-end reads. ">
+ <validator type="regex">[A-Za-z0-9_ :-{}/+|]+</validator>
+ </param>
<param argument="--cut" label="Remove a fixed number of bases" type="integer" min="-100" max="100" value="0" help="This option allows to unconditionally remove bases from the beginning or end of each read. If the given length is positive, the bases are removed from the beginning of each read. If it is negative, the bases are removed from the end." />
<param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
</section>
@@ -575,7 +598,9 @@ $read_mod_options.zero_cap
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="AGATCGGAAGAGC"/>
- <param name="cut" value="5"/>
+ <section name="read_mod_options">
+ <param name="cut" value="5"/>
+ </section>
<output name="out1" file="cutadapt_small_cut.out" ftype="fastq"/>
</test>
<!-- Test rename options -->
@@ -584,17 +609,21 @@ $read_mod_options.zero_cap
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="AGATCGGAAGAGC"/>
- <param name="cut" value="5"/>
- <param name="rename" value="{prefix:1_13_1259/1} barcode={AGATC} adapter={illumina_adapter}"/>
+ <section name="read_mod_options">
+ <param name="cut" value="5"/>
+ <param name="rename" value="{prefix:1_13_1259/1} barcode={AGATC} adapter={illumina_adapter}"/>
+ </section>
<output name="out1" file="cutadapt_small_rename.out" ftype="fastq"/>
</test>
- <!-- Test action options -->
+ <!-- Test action options -->
<test expect_num_outputs="1">
<param name="type" value="single" />
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="CGTCCGAANTAG"/>
- <param name="action" value="retain"/>
+ <section name="adapter_options">
+ <param name="action" value="retain"/>
+ </section>
<output name="out1" file="cutadapt_action_retain.out" ftype="fastq"/>
</test>
<test expect_num_outputs="1">
@@ -602,7 +631,9 @@ $read_mod_options.zero_cap
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="CGTCCGAANTAG"/>
- <param name="action" value="mask"/>
+ <section name="adapter_options">
+ <param name="action" value="mask"/>
+ </section>
<output name="out1" file="cutadapt_action_mask.out" ftype="fastq"/>
</test>
<test expect_num_outputs="1">
@@ -610,7 +641,9 @@ $read_mod_options.zero_cap
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="CGTCCGAANTAG"/>
- <param name="action" value="lowercase"/>
+ <section name="adapter_options">
+ <param name="action" value="lowercase"/>
+ </section>
<output name="out1" file="cutadapt_action_lowercase.out" ftype="fastq"/>
</test>
<test expect_num_outputs="1">
@@ -618,16 +651,20 @@ $read_mod_options.zero_cap
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="CGTCCGAANTAG"/>
- <param name="action" value="none"/>
+ <section name="adapter_options">
+ <param name="action" value="none"/>
+ </section>
<output name="out1" file="cutadapt_action_none.out" ftype="fastq"/>
</test>
- <!-- Test revcomp options -->
+ <!-- Test revcomp options -->
<test expect_num_outputs="1">
<param name="type" value="single" />
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="TAAACAGATTAGT"/>
- <param name="revcomp" value="true"/>
+ <section name="adapter_options">
+ <param name="revcomp" value="true"/>
+ </section>
<output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/>
</test>
<!-- Test minimum lenghth paired-reads -->
@@ -636,14 +673,14 @@ $read_mod_options.zero_cap
<param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
<param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
<param name="adapter_source_list" value="user"/>
- <param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="adapter" value="ATCTGGTTCC"/>
<param name="adapter_source_list2" value="user"/>
- <param name="adapter2" value="AGATCGGAAGAGC"/>
+ <param name="adapter2" value="CTACAAG"/>
<section name="filter_options">
<param name="minimum_length" value="30"/>
<param name="pair_filter" value="both"/>
<conditional name="minimum_options">
- <param name="minimum_r2" value="true"/>
+ <param name="minimum_r2" value="True"/>
<param name="value_minimum" value="10"/>
</conditional>
</section>
@@ -654,7 +691,7 @@ $read_mod_options.zero_cap
<has_text text="--pair-filter=both"/>
</assert_command>
</test>
- <!-- Test maximum lenghth paired-reads -->
+ <!-- Test maximum lenghth paired-reads -->
<test expect_num_outputs="2">
<param name="type" value="paired" />
<param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
@@ -667,7 +704,7 @@ $read_mod_options.zero_cap
<param name="pair_filter" value="both"/>
<param name="maximum_length" value="50"/>
<conditional name="maximum_options">
- <param name="maximum_r2" value="true"/>
+ <param name="maximum_r2" value="True"/>
<param name="value_maximum" value="30"/>
</conditional>
</section>
@@ -678,6 +715,77 @@ $read_mod_options.zero_cap
<has_text text="--pair-filter=both"/>
</assert_command>
</test>
+ <!-- Test length options -->
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGCCGCTANGACG"/>
+ <section name="read_mod_options">
+ <conditional name="shorten_options">
+ <param name="shorten_values" value="True"/>
+ <param name="shorten_end" value="3prime"/>
+ <param name="length" value="10"/>
+ </conditional>
+ </section>
+ <output name="out1" file="cutadapt_shorten_3prime.out" ftype="fastq"/>
+ </test>
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGCCGCTANGACG"/>
+ <section name="read_mod_options">
+ <conditional name="shorten_options">
+ <param name="shorten_values" value="True"/>
+ <param name="shorten_end" value="5prime"/>
+ <param name="length" value="10"/>
+ </conditional>
+ </section>
+ <output name="out1" file="cutadapt_shorten_5prime.out" ftype="fastq"/>
+ </test>
+ <!-- Test max expected errors options -->
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGCGGCTTAGACG"/>
+ <section name="filter_options">
+ <param name="max_expected_errors" value="10"/>
+ </section>
+ <output name="out1" file="cutadapt_shorten_expected_errors.out" ftype="fastq"/>
+ </test>
+ <!-- Test disallow internal adaptors option -->
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="GAANTAGCTACCAC"/>
+ <section name="adapter_options">
+ <param name="internal" value="X"/>
+ </section>
+ <output name="out1" file="cutadapt_shorten_internal_adapters.out" ftype="fastq"/>
+ <assert_command>
+ <has_text text="GAANTAGCTACCACX"/>
+ </assert_command>
+ </test>
+ <test expect_num_outputs="2">
+ <param name="type" value="paired" />
+ <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
+ <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="adapter_source_list2" value="user"/>
+ <param name="adapter2" value="AGATCGGAAGAGC"/>
+ <section name="adapter_options">
+ <param name="internal" value="X"/>
+ </section>
+ <output name="out1" decompress="True" file="cutadapt_out1_internal_adapter.fq.gz" ftype="fastq.gz"/>
+ <output name="out2" decompress="True" file="cutadapt_out2_internal_adapter.fq.gz" ftype="fastq.gz"/>
+ <assert_command>
+ <has_text text="AGATCGGAAGAGCX"/>
+ </assert_command>
+ </test>
</tests>
<help><![CDATA[
diff --git a/tools/cutadapt/macros.xml b/tools/cutadapt/macros.xml
index 9b057d0ecfb..3e3fb1f62b7 100644
--- a/tools/cutadapt/macros.xml
+++ b/tools/cutadapt/macros.xml
@@ -30,13 +30,13 @@
#for $a in $library.r1.adapters
#if $a.adapter_source.adapter_source_list == 'builtin':
- -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}'
+ -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${$adapter_options.internal}'
#else if $a.adapter_source.adapter_source_list == 'file':
- -a file:'${a.adapter_source.adapter_file}'
+ -a file:'${a.adapter_source.adapter_file}${$adapter_options.internal}'
#else if str($a.adapter_source.adapter_name) != "":
- -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}'
+ -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${$adapter_options.internal}'
#else
- -a '${a.adapter_source.adapter}'
+ -a '${a.adapter_source.adapter}${$adapter_options.internal}'
#end if
#end for
#for $aa in $library.r1.anywhere_adapters
@@ -52,13 +52,13 @@
#end for
#for $fa in $library.r1.front_adapters
#if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
- -g '${fa.front_adapter_source.front_adapter.fields.name}'='${fa.front_adapter_source.front_adapter}'
+ -g '${fa.front_adapter_source.front_adapter.fields.name}'='${$adapter_options.internal}${fa.front_adapter_source.front_adapter}'
#else if $fa.front_adapter_source.front_adapter_source_list == 'file':
- -g file:'${fa.front_adapter_source.front_adapter_file}'
+ -g file:'${$adapter_options.internal}${fa.front_adapter_source.front_adapter_file}'
#else if str($fa.front_adapter_source.front_adapter_name) != "":
- -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
+ -g '${$adapter_options.internal}${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
#else
- -g '${fa.front_adapter_source.front_adapter}'
+ -g '${$adapter_options.internal}${fa.front_adapter_source.front_adapter}'
#end if
#end for
@@ -95,13 +95,13 @@
#for $a in $library.r2.adapters2
#if $a.adapter_source2.adapter_source_list2 == 'builtin':
- -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}'
+ -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}${$adapter_options.internal}'
#else if $a.adapter_source2.adapter_source_list2 == 'file':
- -A file:'${a.adapter_source2.adapter_file2}'
+ -A file:'${a.adapter_source2.adapter_file2}${$adapter_options.internal}'
#else if str($a.adapter_source2.adapter_name2) != "":
- -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}'
+ -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}${$adapter_options.internal}'
#else
- -A '${a.adapter_source2.adapter2}'
+ -A '${a.adapter_source2.adapter2}${$adapter_options.internal}'
#end if
#end for
#for $aa in $library.r2.anywhere_adapters2
@@ -117,13 +117,13 @@
#end for
#for $fa in $library.r2.front_adapters2
#if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
- -G '${fa.front_adapter_source2.front_adapter2.fields.name}'='${fa.front_adapter_source2.front_adapter2}'
+ -G '${$adapter_options.internal}${fa.front_adapter_source2.front_adapter2.fields.name}'='${fa.front_adapter_source2.front_adapter2}'
#else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
- -G file:'${fa.front_adapter_source2.front_adapter_file2}'
+ -G file:'${$adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}'
#else if str($fa.front_adapter_source2.front_adapter_name2) != "":
- -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}'
+ -G '${fa.front_adapter_source2.front_adapter_name2}'='${$adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
#else
- -G '${fa.front_adapter_source2.front_adapter2}'
+ -G '${$adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
#end if
#end for
@@ -205,7 +205,7 @@
<param name="adapter_source_list" type="select" label="Source" >
<option value="builtin" selected="True">Standard (select from the list below)</option>
<option value="user">Enter custom sequence</option>
- <option value="file">File From History</option>
+ <option value="file">File from history</option>
</param>
<when value="user">
@@ -306,7 +306,7 @@
<param name="front_adapter_source_list2" type="select" label="Source">
<option value="builtin" selected="True">Standard (select from the list below)</option>
<option value="user">Enter custom sequence</option>
- <option value="file">File From History</option>
+ <option value="file">File from history</option>
</param>
<when value="user">
@@ -327,7 +327,7 @@
<param name="anywhere_adapter_source_list2" type="select" label="Source">
<option value="builtin" selected="True">Standard (select from the list below)</option>
<option value="user">Enter custom sequence</option>
- <option value="file">File From History</option>
+ <option value="file">File from history</option>
</param>
<when value="user">
diff --git a/tools/cutadapt/test-data/A1.fastq.gz b/tools/cutadapt/test-data/A1.fastq.gz
index 1635e3cc999c2a60c131ac85df585770c8fa803d..492819bb7c2ec0a974f8432872ae64d6f0fec966 100644
GIT binary patch
delta 15
Wcmcb@bcKmczMF$#UHe8hKSls3I0T>o
delta 15
Wcmcb@bcKmczMF%=#BC#+A0q%H7X#%0
diff --git a/tools/cutadapt/test-data/A2.fastq.gz b/tools/cutadapt/test-data/A2.fastq.gz
index 4e4bb5ce630e4718f5c87e20e692c25b5d8892e3..05d0507d24c22d52fcc68aacd598568ae43416b3 100644
GIT binary patch
delta 15
WcmX@cbc~5jzMF$#UHe8h2SxxUlmvDF
delta 15
WcmX@cbc~5jzMF%=#BC#+10w(;a|62o
diff --git a/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz b/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz
index 80c3d43467770d941abfbf95029ab645efcbf5d4..b40594d6369aae562e0c2a5b5fc8d9333e4d2d98 100644
GIT binary patch
delta 15
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delta 15
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diff --git a/tools/cutadapt/test-data/cutadapt_out1_internal_adapter.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_internal_adapter.fq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..b4ed3a8e10ab6569dd94ec5cb7afc0b5b223029f
GIT binary patch
literal 12180
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diff --git a/tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz
index 16ee3977765cee609b89cbd42d0a2cc529c51f27..a16e45d105d0a506713ffdb6f8a682aa47a1d43e 100644
GIT binary patch
delta 14
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delta 14
VcmZo;Y-41T@8)2z^P0%k000<517-jK
diff --git a/tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz
index d2b182f3b1876854bdb58d04512afff6988b59ef..0ef6be6da2eca8f837e764165a909c0be1434b25 100644
GIT binary patch
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diff --git a/tools/cutadapt/test-data/cutadapt_out2_max_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_max_length.fq.gz
index 0627bf4b7648059444225466d0ec8a86d3bb8a76..529a6f4d937cbe75cd2098045bfcf6eaf8f152a7 100644
GIT binary patch
delta 14
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delta 14
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diff --git a/tools/cutadapt/test-data/cutadapt_out2_min_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_min_length.fq.gz
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diff --git a/tools/cutadapt/test-data/cutadapt_shorten_3prime.out b/tools/cutadapt/test-data/cutadapt_shorten_3prime.out
new file mode 100644
index 00000000000..3e27035a57f
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_shorten_3prime.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANT
++
+)3%)&&&&!.
+@prefix:1_13_1259/1
+
++
+
+@prefix:1_13_1440/1
+CAAGATCTNC
++
+<=A:A=57!7
diff --git a/tools/cutadapt/test-data/cutadapt_shorten_5prime.out b/tools/cutadapt/test-data/cutadapt_shorten_5prime.out
new file mode 100644
index 00000000000..538740e4dc4
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_shorten_5prime.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+TTAGACAAAT
++
+75)'77&&&5
+@prefix:1_13_1259/1
+
++
+
+@prefix:1_13_1440/1
+CTAGTTAAAC
++
+)71>70<,=:
diff --git a/tools/cutadapt/test-data/cutadapt_shorten_expected_errors.out b/tools/cutadapt/test-data/cutadapt_shorten_expected_errors.out
new file mode 100644
index 00000000000..767ca2279af
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_shorten_expected_errors.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:
diff --git a/tools/cutadapt/test-data/cutadapt_shorten_internal_adapters.out b/tools/cutadapt/test-data/cutadapt_shorten_internal_adapters.out
new file mode 100644
index 00000000000..767ca2279af
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_shorten_internal_adapters.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:
diff --git a/tools/cutadapt/test-data/cutadapt_trimmed.out.gz b/tools/cutadapt/test-data/cutadapt_trimmed.out.gz
index 5adaf22b4068071be4ac95d0fb38fbfba90a0c6f..93b0776b83e4d7d56e7ac6cafa6296f276fbd8a2 100644
GIT binary patch
delta 15
WcmbQqGLwZ(zMF&LcKb#)VI}|~kpv+C
delta 15
WcmbQqGLwZ(zMF#~(QPA}FcSbCa06xl
diff --git a/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz b/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz
index 6b9e56db4e06c688287bfdc6fca4151e87173fea..120f3cc6a7db5774923b471ac4b7c31ed1ab93bb 100644
GIT binary patch
delta 15
WcmdlVw?B?ezMF&LcKb#)OML(^Rt0nb
delta 15
WcmdlVw?B?ezMF#~(QPA}r9J>GH3Yc;
diff --git a/tools/cutadapt/test-data/unknown.fastq.gz b/tools/cutadapt/test-data/unknown.fastq.gz
index 13b4154300f7aaa2371c3eb1d1254d55ab0d0ba2..2683cff111cb220de1b621038e140b18258ad2e9 100644
GIT binary patch
delta 14
VcmZ3>xR#MkzMF$#UHe3~<p3Xp1c(3t
delta 14
VcmZ3>xR#MkzMF%=#BCzmasV711I+*c
From 318f03d8014617457ddc35bd3698dfee5deee872 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 22:13:42 +0200
Subject: [PATCH 08/20] Add building internal adaptor tests and fix typo
---
tools/cutadapt/cutadapt.xml | 10 ++++++
tools/cutadapt/macros.xml | 32 +++++++++---------
tools/cutadapt/test-data/A1.fastq.gz | Bin 340 -> 340 bytes
tools/cutadapt/test-data/A2.fastq.gz | Bin 326 -> 326 bytes
.../cutadapt_builtin_internal_adapter.out | 12 +++++++
.../test-data/cutadapt_nextseq_out.fq.gz | Bin 12158 -> 12158 bytes
.../cutadapt_out1_internal_adapter.fq.gz | Bin 12180 -> 12180 bytes
.../test-data/cutadapt_out1_max_length.fq.gz | Bin 134 -> 134 bytes
.../test-data/cutadapt_out1_min_length.fq.gz | Bin 9298 -> 9298 bytes
.../cutadapt_out2_internal_adapter.fq.gz | Bin 12153 -> 12153 bytes
.../test-data/cutadapt_out2_max_length.fq.gz | Bin 139 -> 139 bytes
.../test-data/cutadapt_out2_min_length.fq.gz | Bin 10480 -> 10480 bytes
.../test-data/cutadapt_trimmed.out.gz | Bin 537 -> 537 bytes
.../test-data/cutadapt_untrimmed.out.gz | Bin 12095 -> 12095 bytes
tools/cutadapt/test-data/unknown.fastq.gz | Bin 173 -> 173 bytes
15 files changed, 38 insertions(+), 16 deletions(-)
create mode 100644 tools/cutadapt/test-data/cutadapt_builtin_internal_adapter.out
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 300970a96a8..c3a2ba4c7f2 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -786,6 +786,16 @@ $read_mod_options.zero_cap
<has_text text="AGATCGGAAGAGCX"/>
</assert_command>
</test>
+ <test expect_num_outputs="1">
+ <param name="type" value="single" />
+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+ <param name="adapter_source_list" value="builtin"/>
+ <param name="adapter" value="TGTAGGCC"/>
+ <section name="adapter_options">
+ <param name="internal" value="X"/>
+ </section>
+ <output name="out1" file="cutadapt_builtin_internal_adapter.out" ftype="fastq"/>
+ </test>
</tests>
<help><![CDATA[
diff --git a/tools/cutadapt/macros.xml b/tools/cutadapt/macros.xml
index 3e3fb1f62b7..684f6cf1fdf 100644
--- a/tools/cutadapt/macros.xml
+++ b/tools/cutadapt/macros.xml
@@ -30,13 +30,13 @@
#for $a in $library.r1.adapters
#if $a.adapter_source.adapter_source_list == 'builtin':
- -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${$adapter_options.internal}'
+ -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${adapter_options.internal}'
#else if $a.adapter_source.adapter_source_list == 'file':
- -a file:'${a.adapter_source.adapter_file}${$adapter_options.internal}'
+ -a file:'${a.adapter_source.adapter_file}${adapter_options.internal}'
#else if str($a.adapter_source.adapter_name) != "":
- -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${$adapter_options.internal}'
+ -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${adapter_options.internal}'
#else
- -a '${a.adapter_source.adapter}${$adapter_options.internal}'
+ -a '${a.adapter_source.adapter}${adapter_options.internal}'
#end if
#end for
#for $aa in $library.r1.anywhere_adapters
@@ -52,13 +52,13 @@
#end for
#for $fa in $library.r1.front_adapters
#if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
- -g '${fa.front_adapter_source.front_adapter.fields.name}'='${$adapter_options.internal}${fa.front_adapter_source.front_adapter}'
+ -g '${fa.front_adapter_source.front_adapter.fields.name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
#else if $fa.front_adapter_source.front_adapter_source_list == 'file':
- -g file:'${$adapter_options.internal}${fa.front_adapter_source.front_adapter_file}'
+ -g file:'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}'
#else if str($fa.front_adapter_source.front_adapter_name) != "":
- -g '${$adapter_options.internal}${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
+ -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
#else
- -g '${$adapter_options.internal}${fa.front_adapter_source.front_adapter}'
+ -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
#end if
#end for
@@ -95,13 +95,13 @@
#for $a in $library.r2.adapters2
#if $a.adapter_source2.adapter_source_list2 == 'builtin':
- -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}${$adapter_options.internal}'
+ -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}${adapter_options.internal}'
#else if $a.adapter_source2.adapter_source_list2 == 'file':
- -A file:'${a.adapter_source2.adapter_file2}${$adapter_options.internal}'
+ -A file:'${a.adapter_source2.adapter_file2}${adapter_options.internal}'
#else if str($a.adapter_source2.adapter_name2) != "":
- -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}${$adapter_options.internal}'
+ -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}${adapter_options.internal}'
#else
- -A '${a.adapter_source2.adapter2}${$adapter_options.internal}'
+ -A '${a.adapter_source2.adapter2}${adapter_options.internal}'
#end if
#end for
#for $aa in $library.r2.anywhere_adapters2
@@ -117,13 +117,13 @@
#end for
#for $fa in $library.r2.front_adapters2
#if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
- -G '${$adapter_options.internal}${fa.front_adapter_source2.front_adapter2.fields.name}'='${fa.front_adapter_source2.front_adapter2}'
+ -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2.fields.name}'='${fa.front_adapter_source2.front_adapter2}'
#else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
- -G file:'${$adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}'
+ -G file:'${adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}'
#else if str($fa.front_adapter_source2.front_adapter_name2) != "":
- -G '${fa.front_adapter_source2.front_adapter_name2}'='${$adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
+ -G '${fa.front_adapter_source2.front_adapter_name2}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
#else
- -G '${$adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
+ -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
#end if
#end for
diff --git a/tools/cutadapt/test-data/A1.fastq.gz b/tools/cutadapt/test-data/A1.fastq.gz
index 492819bb7c2ec0a974f8432872ae64d6f0fec966..8f0e0602b2edc9ec86dca2ff4ae24271e6dde556 100644
GIT binary patch
delta 15
Wcmcb@bcKmczMF$#>ZFZqevAMo*#wdR
delta 15
Wcmcb@bcKmczMF$#UHe8hKSls3I0T>o
diff --git a/tools/cutadapt/test-data/A2.fastq.gz b/tools/cutadapt/test-data/A2.fastq.gz
index 05d0507d24c22d52fcc68aacd598568ae43416b3..91aab83a1f1f29c1522a15348a9d4a323feb37e6 100644
GIT binary patch
delta 15
WcmX@cbc~5jzMF$#>ZFZq4vYXMH3Vn?
delta 15
WcmX@cbc~5jzMF$#UHe8h2SxxUlmvDF
diff --git a/tools/cutadapt/test-data/cutadapt_builtin_internal_adapter.out b/tools/cutadapt/test-data/cutadapt_builtin_internal_adapter.out
new file mode 100644
index 00000000000..767ca2279af
--- /dev/null
+++ b/tools/cutadapt/test-data/cutadapt_builtin_internal_adapter.out
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:
diff --git a/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz b/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz
index b40594d6369aae562e0c2a5b5fc8d9333e4d2d98..0da18600442eb77c5a04f3e5019c125b810ac105 100644
GIT binary patch
delta 15
Wcmewt_b-l3zMF#~e9}g?3Vi@H*9Eu$
delta 15
Wcmewt_b-l3zMF#~w|yg9g+2f^Bn86&
diff --git a/tools/cutadapt/test-data/cutadapt_out1_internal_adapter.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_internal_adapter.fq.gz
index b4ed3a8e10ab6569dd94ec5cb7afc0b5b223029f..bc650c71568f3ca6d7ca91bd750a30c923ce0614 100644
GIT binary patch
delta 15
WcmbOdKP8?`zMF$#-{g&Kefj_^^aW%9
delta 15
WcmbOdKP8?`zMF&LUC&0gK79Zz@db?l
diff --git a/tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz
index a16e45d105d0a506713ffdb6f8a682aa47a1d43e..6d58cd3faa479de074762fcc3731fde04d341337 100644
GIT binary patch
delta 14
VcmZo;Y-41T@8)30o;;DQ0RS3D1Ka=r
delta 14
VcmZo;Y-41T@8)2r@0iHe000_)1LXh!
diff --git a/tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz
index 0ef6be6da2eca8f837e764165a909c0be1434b25..24c44a5297ed627e3c4a0d07986c76dfb2a2dfe7 100644
GIT binary patch
delta 15
WcmccQamj;CzMF#~VDd&b9~A&CLj?B#
delta 15
WcmccQamj;CzMF#~y<;Prj|u=SmIVU<
diff --git a/tools/cutadapt/test-data/cutadapt_out2_internal_adapter.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_internal_adapter.fq.gz
index 48e71cfd240df2961fa98bb22fa9bcac22c57037..ec55e23048948ef8a7ae93a946d3370c18e5918d 100644
GIT binary patch
delta 15
Wcmewv_cM-7zMF$#-{g&K#rgm?um%wT
delta 15
Wcmewv_cM-7zMF&LUC&0gVtoKNtp+*(
diff --git a/tools/cutadapt/test-data/cutadapt_out2_max_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_max_length.fq.gz
index 529a6f4d937cbe75cd2098045bfcf6eaf8f152a7..5c1a596e45f5e308a279f3b7ab1be6fa9efde8ea 100644
GIT binary patch
delta 14
VcmeBX>}F(>@8)30o;;DQ6#yE}1M2_)
delta 14
VcmeBX>}F(>@8)2r@0iHe3IH1h1M~m@
diff --git a/tools/cutadapt/test-data/cutadapt_out2_min_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_min_length.fq.gz
index c96771ab1c9ea21d7122667dcff02b8548dcbfc4..94d1667e121e24de2c345cd92c2a57511de71cb0 100644
GIT binary patch
delta 15
Wcmewm_#u!@zMF#~VDd(`R~i5^wFTz@
delta 15
Wcmewm_#u!@zMF#~y<;QWD-8fM2nF*1
diff --git a/tools/cutadapt/test-data/cutadapt_trimmed.out.gz b/tools/cutadapt/test-data/cutadapt_trimmed.out.gz
index 93b0776b83e4d7d56e7ac6cafa6296f276fbd8a2..a2a91ad9f008ef1b9d0bcaa9e625254e636187ae 100644
GIT binary patch
delta 15
WcmbQqGLwZ(zMF&L;G~Ug!b|`nECdn&
delta 15
WcmbQqGLwZ(zMF&LcKb#)VI}|~kpv+C
diff --git a/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz b/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz
index 120f3cc6a7db5774923b471ac4b7c31ed1ab93bb..26b630e33125f8c2aa4b51a2f2e23d16e01c4ca1 100644
GIT binary patch
delta 15
WcmdlVw?B?ezMF&L;G~UgmihoM@daf7
delta 15
WcmdlVw?B?ezMF&LcKb#)OML(^Rt0nb
diff --git a/tools/cutadapt/test-data/unknown.fastq.gz b/tools/cutadapt/test-data/unknown.fastq.gz
index 2683cff111cb220de1b621038e140b18258ad2e9..4edef7b57a5bade2bf8d1f85b6a687b29fe4520b 100644
GIT binary patch
delta 14
VcmZ3>xR#MkzMF$#>ZFNm%K;xU1bP4f
delta 14
VcmZ3>xR#MkzMF$#UHe3~<p3Xp1c(3t
From ef51a2276b394640238239a03f2c30ba8416c1c7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 22:15:34 +0200
Subject: [PATCH 09/20] Include assertion internal adaptor building test
---
tools/cutadapt/cutadapt.xml | 3 +++
1 file changed, 3 insertions(+)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index c3a2ba4c7f2..bebebf3becb 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -795,6 +795,9 @@ $read_mod_options.zero_cap
<param name="internal" value="X"/>
</section>
<output name="out1" file="cutadapt_builtin_internal_adapter.out" ftype="fastq"/>
+ <assert_command>
+ <has_text text="TGTAGGCCX"/>
+ </assert_command>
</test>
</tests>
From cb896d3140d29c1f8ffcebdbadf59bb8deceec5b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 22:18:29 +0200
Subject: [PATCH 10/20] Modify cut parameter
---
tools/cutadapt/cutadapt.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index bebebf3becb..7583c897d05 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -288,7 +288,7 @@ $read_mod_options.zero_cap
<param argument="--rename" label="Rename reads" type="text" optional="True" help="This option can be used to rename both single-end and paired-end reads. ">
<validator type="regex">[A-Za-z0-9_ :-{}/+|]+</validator>
</param>
- <param argument="--cut" label="Remove a fixed number of bases" type="integer" min="-100" max="100" value="0" help="This option allows to unconditionally remove bases from the beginning or end of each read. If the given length is positive, the bases are removed from the beginning of each read. If it is negative, the bases are removed from the end." />
+ <param argument="--cut" label="Remove a fixed number of bases" type="integer" value="0" help="This option allows to unconditionally remove bases from the beginning or end of each read. If the given length is positive, the bases are removed from the beginning of each read. If it is negative, the bases are removed from the end." />
<param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
</section>
From b0e6e14028419a4cc172d399c00e2418e5723480 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Tue, 1 Jun 2021 22:25:02 +0200
Subject: [PATCH 11/20] Include information in help field
---
tools/cutadapt/cutadapt.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 7583c897d05..cfed29ba3e4 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -204,7 +204,7 @@ $read_mod_options.zero_cap
<option value="lowercase">Lowercase: convert to lowercase</option>
<option value="none">None: leave unchanged</option>
</param>
- <param name="internal" type="select" label="Disallow internal adaptor ocurrences" help="TODO">
+ <param name="internal" type="select" label="Disallow internal adaptor ocurrences" help="The non-internal 5’ and 3’ adapter types disallow internal occurrences of the adapter sequence. The adapter must always be at one of the ends of the read, but partial occurrences are also ok.">
<option value="X">Enabled</option>
<option value="" selected="True">Disabled</option>
</param>
From 76b023454e24e2dda8462cf43fce42ac64163807 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Wed, 2 Jun 2021 17:09:52 +0200
Subject: [PATCH 12/20] Add sanitize --length-tag
---
tools/cutadapt/cutadapt.xml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index cfed29ba3e4..2b0a7bdbe75 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -284,7 +284,9 @@ $read_mod_options.zero_cap
<when value="False">
</when>
</conditional>
- <param argument="--length-tag" label="Length Tag" type="text" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." />
+ <param argument="--length-tag" label="Length tag" type="text" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." >
+ <validator type="regex">[A-Za-z_= :]+</validator>
+ </param>
<param argument="--rename" label="Rename reads" type="text" optional="True" help="This option can be used to rename both single-end and paired-end reads. ">
<validator type="regex">[A-Za-z0-9_ :-{}/+|]+</validator>
</param>
From 028015260b29f519317f3ec5f69db0c101d1d035 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Wed, 2 Jun 2021 19:47:51 +0200
Subject: [PATCH 13/20] Add sanitizers
---
tools/cutadapt/cutadapt.xml | 31 ++++++++++++++++--
tools/cutadapt/macros.xml | 2 +-
tools/cutadapt/test-data/A1.fastq.gz | Bin 340 -> 340 bytes
tools/cutadapt/test-data/A2.fastq.gz | Bin 326 -> 326 bytes
.../test-data/cutadapt_nextseq_out.fq.gz | Bin 12158 -> 12158 bytes
.../cutadapt_out1_internal_adapter.fq.gz | Bin 12180 -> 12180 bytes
.../test-data/cutadapt_out1_max_length.fq.gz | Bin 134 -> 134 bytes
.../test-data/cutadapt_out1_min_length.fq.gz | Bin 9298 -> 9298 bytes
.../cutadapt_out2_internal_adapter.fq.gz | Bin 12153 -> 12153 bytes
.../test-data/cutadapt_out2_max_length.fq.gz | Bin 139 -> 139 bytes
.../test-data/cutadapt_out2_min_length.fq.gz | Bin 10480 -> 10480 bytes
.../test-data/cutadapt_small_rename.out | 6 ++--
.../test-data/cutadapt_trimmed.out.gz | Bin 537 -> 537 bytes
.../test-data/cutadapt_untrimmed.out.gz | Bin 12095 -> 12095 bytes
tools/cutadapt/test-data/unknown.fastq.gz | Bin 173 -> 173 bytes
15 files changed, 32 insertions(+), 7 deletions(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 2b0a7bdbe75..00fc4d22ec7 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -285,10 +285,34 @@ $read_mod_options.zero_cap
</when>
</conditional>
<param argument="--length-tag" label="Length tag" type="text" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." >
- <validator type="regex">[A-Za-z_= :]+</validator>
+ <sanitizer invalid_char="">
+ <valid initial="string.letters,string.digits">
+ <add value="_" />
+ <add value=":" />
+ <add value=" " />
+ <add value="{" />
+ <add value="}" />
+ <add value="/" />
+ <add value="+" />
+ <add value="|" />
+ <add value="=" />
+ </valid>
+ </sanitizer>
</param>
<param argument="--rename" label="Rename reads" type="text" optional="True" help="This option can be used to rename both single-end and paired-end reads. ">
- <validator type="regex">[A-Za-z0-9_ :-{}/+|]+</validator>
+ <sanitizer invalid_char="">
+ <valid initial="string.letters,string.digits">
+ <add value="_" />
+ <add value=":" />
+ <add value=" " />
+ <add value="{" />
+ <add value="}" />
+ <add value="/" />
+ <add value="+" />
+ <add value="|" />
+ <add value="=" />
+ </valid>
+ </sanitizer>
</param>
<param argument="--cut" label="Remove a fixed number of bases" type="integer" value="0" help="This option allows to unconditionally remove bases from the beginning or end of each read. If the given length is positive, the bases are removed from the beginning of each read. If it is negative, the bases are removed from the end." />
<param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
@@ -611,9 +635,10 @@ $read_mod_options.zero_cap
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="adapter_name" value="test_adapter"/>
<section name="read_mod_options">
<param name="cut" value="5"/>
- <param name="rename" value="{prefix:1_13_1259/1} barcode={AGATC} adapter={illumina_adapter}"/>
+ <param name="rename" value="{id} barcode={cut_prefix}"/>
</section>
<output name="out1" file="cutadapt_small_rename.out" ftype="fastq"/>
</test>
diff --git a/tools/cutadapt/macros.xml b/tools/cutadapt/macros.xml
index 684f6cf1fdf..a6d71a25055 100644
--- a/tools/cutadapt/macros.xml
+++ b/tools/cutadapt/macros.xml
@@ -56,7 +56,7 @@
#else if $fa.front_adapter_source.front_adapter_source_list == 'file':
-g file:'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}'
#else if str($fa.front_adapter_source.front_adapter_name) != "":
- -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
+ -g '${fa.front_adapter_source.front_adapter_name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
#else
-g '${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
#end if
diff --git a/tools/cutadapt/test-data/A1.fastq.gz b/tools/cutadapt/test-data/A1.fastq.gz
index 8f0e0602b2edc9ec86dca2ff4ae24271e6dde556..f25c3f0139f99399a5142fa123d94e24947f348f 100644
GIT binary patch
delta 16
Xcmcb@bcKmszMF&L$nNbM*?k!SF+>HT
delta 16
Xcmcb@bcKmszMF$#>ZENO*?k!SF8~Ee
diff --git a/tools/cutadapt/test-data/A2.fastq.gz b/tools/cutadapt/test-data/A2.fastq.gz
index 91aab83a1f1f29c1522a15348a9d4a323feb37e6..6f330e0d5bf1cd61363591f43b09d3334b975f59 100644
GIT binary patch
delta 16
XcmX@cbc~5zzMF&L$nNbM+3gttFN6hn
delta 16
XcmX@cbc~5zzMF$#>ZENO+3gttEkFey
diff --git a/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz b/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz
index 0da18600442eb77c5a04f3e5019c125b810ac105..cc457262169a6c961f90f8e5a2c7fd773a127223 100644
GIT binary patch
delta 16
Xcmewt_b-lJzMF%gY4`Sx?B)6ZKJ*5}
delta 16
Xcmewt_b-lJzMF#~eA2d!?B)6ZJj@1f
diff --git a/tools/cutadapt/test-data/cutadapt_out1_internal_adapter.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_internal_adapter.fq.gz
index bc650c71568f3ca6d7ca91bd750a30c923ce0614..01f0c7e2d8749a92d7932dd40c8f4cdd4d47d76e 100644
GIT binary patch
delta 16
XcmbOdKP8@BzMF&L;hyaq*?aW?HE#xJ
delta 16
XcmbOdKP8@BzMF$#-{fr@*?aW?Gk*pf
diff --git a/tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz
index 6d58cd3faa479de074762fcc3731fde04d341337..15de53bf4209c1a535dc9b89d9ee03fadab1b333 100644
GIT binary patch
delta 15
WcmZo;Y-41X@8)3W-m`rodp!Ulfdt(E
delta 15
WcmZo;Y-41X@8)30p1f@$dp!Uj@C1_p
diff --git a/tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz
index 24c44a5297ed627e3c4a0d07986c76dfb2a2dfe7..f2fa55b88f608eda29d044f4b4f90206e9bbc5c2 100644
GIT binary patch
delta 16
XcmccQamj;SzMF%gXwUYI?A|H>HkSqZ
delta 16
XcmccQamj;SzMF#~VDh$&?A|H>G_D1%
diff --git a/tools/cutadapt/test-data/cutadapt_out2_internal_adapter.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_internal_adapter.fq.gz
index ec55e23048948ef8a7ae93a946d3370c18e5918d..3fa45067c977a604d2f7f7a56c6176e04b48dc96 100644
GIT binary patch
delta 16
Xcmewv_cM-NzMF&L;hyaq*^Bf6K=TI`
delta 16
Xcmewv_cM-NzMF$#-{fr@*^Bf6KLZBH
diff --git a/tools/cutadapt/test-data/cutadapt_out2_max_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_max_length.fq.gz
index 5c1a596e45f5e308a279f3b7ab1be6fa9efde8ea..a70dec1ce1f1c107cd9eba84799c9da363d19083 100644
GIT binary patch
delta 15
WcmeBX>}F(_@8)3W-m`rodkX*}5(Ml3
delta 15
WcmeBX>}F(_@8)30p1f@$dkX*{fdrxe
diff --git a/tools/cutadapt/test-data/cutadapt_out2_min_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_min_length.fq.gz
index 94d1667e121e24de2c345cd92c2a57511de71cb0..81c5f8d1109df9cecec4e7019b94538ecf01fd0c 100644
GIT binary patch
delta 16
Xcmewm_#u#8zMF%gXwUYI>@PI{JXZ$l
delta 16
Xcmewm_#u#8zMF#~VDh$&>@PI{I&KD@
diff --git a/tools/cutadapt/test-data/cutadapt_small_rename.out b/tools/cutadapt/test-data/cutadapt_small_rename.out
index 59c665cdb87..9f9c7f26803 100644
--- a/tools/cutadapt/test-data/cutadapt_small_rename.out
+++ b/tools/cutadapt/test-data/cutadapt_small_rename.out
@@ -1,12 +1,12 @@
-@__oc__prefix:1_13_1259/1__cc__ barcode=__oc__AGATC__cc__ adapter=__oc__illumina_adapter__cc__
+@prefix:1_13_573/1 barcode=CGTCC
GAANTAGCTACCACCCTGATTAGACAAAT
+
&&&!.1&(6:<'67..*,:75)'77&&&5
-@__oc__prefix:1_13_1259/1__cc__ barcode=__oc__AGATC__cc__ adapter=__oc__illumina_adapter__cc__
+@prefix:1_13_1259/1 barcode=AGCCG
CTANGACGGGTTGGCCCTTAGACGTATCT
+
A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
-@__oc__prefix:1_13_1259/1__cc__ barcode=__oc__AGATC__cc__ adapter=__oc__illumina_adapter__cc__
+@prefix:1_13_1440/1 barcode=CAAGA
TCTNCCCTGCCACATTGCCCTAGTTAAAC
+
=57!7<';<6?5;;6:+:=)71>70<,=:
diff --git a/tools/cutadapt/test-data/cutadapt_trimmed.out.gz b/tools/cutadapt/test-data/cutadapt_trimmed.out.gz
index a2a91ad9f008ef1b9d0bcaa9e625254e636187ae..33196cc42ab29a21434fee896e5fe41cc4f615d3 100644
GIT binary patch
delta 16
XcmbQqGLwZ}zMF&L!|v@H*@c(@D^Ud^
delta 16
XcmbQqGLwZ}zMF&L;G}IE*@c(@DGdb4
diff --git a/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz b/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz
index 26b630e33125f8c2aa4b51a2f2e23d16e01c4ca1..6a54f5bfb7adf9f600211ca823ed1e2d7e0e2335 100644
GIT binary patch
delta 16
XcmdlVw?B?uzMF&L!|v@H*)8+|Iu-_X
delta 16
XcmdlVw?B?uzMF&L;G}IE*)8+|H_`?i
diff --git a/tools/cutadapt/test-data/unknown.fastq.gz b/tools/cutadapt/test-data/unknown.fastq.gz
index 4edef7b57a5bade2bf8d1f85b6a687b29fe4520b..6741330278cdf0f82b13df1aea4565f1b7921986 100644
GIT binary patch
delta 15
XcmZ3>xR#M!zMF&L$nNbE*_QzTCp`s<
delta 15
XcmZ3>xR#M!zMF$#>ZENG*_QzTB~k@3
From 6fd4d309b2d157c16bd915ecc35021a385cb9411 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Wed, 2 Jun 2021 21:18:35 +0200
Subject: [PATCH 14/20] Add validators
---
tools/cutadapt/cutadapt.xml | 27 +++++++++++++--------------
1 file changed, 13 insertions(+), 14 deletions(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 00fc4d22ec7..646ca305445 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -265,6 +265,7 @@ $read_mod_options.zero_cap
<sanitizer>
<valid initial="string.digits"><add value="," /></valid>
</sanitizer>
+ <validator type="regex">[0-9,]+</validator>
</param>
<param argument="--nextseq-trim" type="integer" value="0" label="NextSeq trimming" help="Experimental option for quality trimming of NextSeq data. This is necessary because that machine cannot distinguish between G and reaching the end of the fragment (it encodes G as ‘black’). This option works like regular quality trimming (where one would use -q 20 instead), except that the qualities of G bases are ignored." />
<param argument="--trim-n" type="boolean" truevalue="--trim-n" falsevalue="" checked="False" label="Trim Ns" help="Trim N's on ends of reads." />
@@ -284,35 +285,29 @@ $read_mod_options.zero_cap
<when value="False">
</when>
</conditional>
- <param argument="--length-tag" label="Length tag" type="text" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." >
+ <param argument="--length-tag" label="Length tag" type="text" optional="True" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." >
<sanitizer invalid_char="">
<valid initial="string.letters,string.digits">
- <add value="_" />
- <add value=":" />
- <add value=" " />
- <add value="{" />
- <add value="}" />
<add value="/" />
<add value="+" />
- <add value="|" />
+ <add value="-" />
<add value="=" />
+ <add value=" " />
</valid>
</sanitizer>
+ <validator type="regex">[A-Za-z0-9 ]+</validator>
</param>
<param argument="--rename" label="Rename reads" type="text" optional="True" help="This option can be used to rename both single-end and paired-end reads. ">
<sanitizer invalid_char="">
<valid initial="string.letters,string.digits">
- <add value="_" />
- <add value=":" />
- <add value=" " />
<add value="{" />
<add value="}" />
- <add value="/" />
- <add value="+" />
- <add value="|" />
+ <add value="_" />
<add value="=" />
+ <add value=" " />
</valid>
</sanitizer>
+ <validator type="regex">[A-Za-z0-9 {}=]+</validator>
</param>
<param argument="--cut" label="Remove a fixed number of bases" type="integer" value="0" help="This option allows to unconditionally remove bases from the beginning or end of each read. If the given length is positive, the bases are removed from the beginning of each read. If it is negative, the bases are removed from the end." />
<param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
@@ -640,7 +635,11 @@ $read_mod_options.zero_cap
<param name="cut" value="5"/>
<param name="rename" value="{id} barcode={cut_prefix}"/>
</section>
- <output name="out1" file="cutadapt_small_rename.out" ftype="fastq"/>
+ <output name="out1" file="cutadapt_small_rename.out" ftype="fastq">
+ <assert_contents>
+ <has_line line="@prefix:1_13_573/1 barcode=CGTCCGAANT"/>
+ </assert_contents>
+ </output>
</test>
<!-- Test action options -->
<test expect_num_outputs="1">
From 60e903ab9e15806868c6628d1a15ffab065b28ee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Wed, 2 Jun 2021 21:32:55 +0200
Subject: [PATCH 15/20] Update validators
---
tools/cutadapt/cutadapt.xml | 5 +++--
tools/cutadapt/test-data/A1.fastq.gz | Bin 340 -> 340 bytes
tools/cutadapt/test-data/A2.fastq.gz | Bin 326 -> 326 bytes
.../test-data/cutadapt_nextseq_out.fq.gz | Bin 12158 -> 12158 bytes
.../cutadapt_out1_internal_adapter.fq.gz | Bin 12180 -> 12180 bytes
.../test-data/cutadapt_out1_max_length.fq.gz | Bin 134 -> 134 bytes
.../test-data/cutadapt_out1_min_length.fq.gz | Bin 9298 -> 9298 bytes
.../cutadapt_out2_internal_adapter.fq.gz | Bin 12153 -> 12153 bytes
.../test-data/cutadapt_out2_max_length.fq.gz | Bin 139 -> 139 bytes
.../test-data/cutadapt_out2_min_length.fq.gz | Bin 10480 -> 10480 bytes
.../test-data/cutadapt_trimmed.out.gz | Bin 537 -> 537 bytes
.../test-data/cutadapt_untrimmed.out.gz | Bin 12095 -> 12095 bytes
tools/cutadapt/test-data/unknown.fastq.gz | Bin 173 -> 173 bytes
13 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 646ca305445..f928a804f86 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -293,9 +293,10 @@ $read_mod_options.zero_cap
<add value="-" />
<add value="=" />
<add value=" " />
+ <add value="_" />
</valid>
</sanitizer>
- <validator type="regex">[A-Za-z0-9 ]+</validator>
+ <validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
</param>
<param argument="--rename" label="Rename reads" type="text" optional="True" help="This option can be used to rename both single-end and paired-end reads. ">
<sanitizer invalid_char="">
@@ -307,7 +308,7 @@ $read_mod_options.zero_cap
<add value=" " />
</valid>
</sanitizer>
- <validator type="regex">[A-Za-z0-9 {}=]+</validator>
+ <validator type="regex">[A-Za-z0-9 {}=_]+</validator>
</param>
<param argument="--cut" label="Remove a fixed number of bases" type="integer" value="0" help="This option allows to unconditionally remove bases from the beginning or end of each read. If the given length is positive, the bases are removed from the beginning of each read. If it is negative, the bases are removed from the end." />
<param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
diff --git a/tools/cutadapt/test-data/A1.fastq.gz b/tools/cutadapt/test-data/A1.fastq.gz
index f25c3f0139f99399a5142fa123d94e24947f348f..03492d7521dba44735a0a31ee755097cc4c31891 100644
GIT binary patch
delta 15
Wcmcb@bcKmczMF%g{MJS`KSls3jRd>^
delta 15
Wcmcb@bcKmczMF&L$nK47evAMqzy#_5
diff --git a/tools/cutadapt/test-data/A2.fastq.gz b/tools/cutadapt/test-data/A2.fastq.gz
index 6f330e0d5bf1cd61363591f43b09d3334b975f59..862538c9ca9a16ef0b17742168a3c8a0eda1bc22 100644
GIT binary patch
delta 15
WcmX@cbc~5jzMF%g{MJS`2SxxU=>(Dh
delta 15
WcmX@cbc~5jzMF&L$nK474vYXO90b4s
diff --git a/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz b/tools/cutadapt/test-data/cutadapt_nextseq_out.fq.gz
index cc457262169a6c961f90f8e5a2c7fd773a127223..4eefe56e57f286e5720c12168ce5f6354b05d0f6 100644
GIT binary patch
delta 15
Wcmewt_b-l3zMF%=?AAuM3Vi@Ic?I79
delta 15
Wcmewt_b-l3zMF%gY4=993Vi@JrUncE
diff --git a/tools/cutadapt/test-data/cutadapt_out1_internal_adapter.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_internal_adapter.fq.gz
index 01f0c7e2d8749a92d7932dd40c8f4cdd4d47d76e..07322b59dc31f067bb394e98b87adf88b0ae6173 100644
GIT binary patch
delta 15
WcmbOdKP8?`zMF$#&h3qCefj__kOhhW
delta 15
WcmbOdKP8?`zMF&L;hv3befj_`lLfE<
diff --git a/tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_max_length.fq.gz
index 15de53bf4209c1a535dc9b89d9ee03fadab1b333..ada41ca50c3d9bb31ab0df4a3f9a9e6d0ef232a5 100644
GIT binary patch
delta 14
VcmZo;Y-41T@8)1|yFHPu0RS4V1OEU3
delta 14
VcmZo;Y-41T@8)3W-ZPP{0RS6|1SJ3f
diff --git a/tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out1_min_length.fq.gz
index f2fa55b88f608eda29d044f4b4f90206e9bbc5c2..b2964928c0076e8f7d3b9c6bfa328ff682fd312a 100644
GIT binary patch
delta 15
WcmccQamj;CzMF$V@AgJE9~A&C-vu22
delta 15
WcmccQamj;CzMF%gXwODA9~A&D+yz1a
diff --git a/tools/cutadapt/test-data/cutadapt_out2_internal_adapter.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_internal_adapter.fq.gz
index 3fa45067c977a604d2f7f7a56c6176e04b48dc96..2ae9229536395f0f39e17f8546c73ef94b0d55ef 100644
GIT binary patch
delta 15
Wcmewv_cM-7zMF$#&h3qC#rgm@Oa?aq
delta 15
Wcmewv_cM-7zMF&L;hv3b#rgm^PX=88
diff --git a/tools/cutadapt/test-data/cutadapt_out2_max_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_max_length.fq.gz
index a70dec1ce1f1c107cd9eba84799c9da363d19083..955f2637794679e39c460e0dc3aa17759cbab91e 100644
GIT binary patch
delta 14
VcmeBX>}F(>@8)1|yFHPu6#yGG1P%ZI
delta 14
VcmeBX>}F(>@8)3W-ZPP{6#yI(1T+8u
diff --git a/tools/cutadapt/test-data/cutadapt_out2_min_length.fq.gz b/tools/cutadapt/test-data/cutadapt_out2_min_length.fq.gz
index 81c5f8d1109df9cecec4e7019b94538ecf01fd0c..894f86195bc77198611a15f2b1ea56276b335faa 100644
GIT binary patch
delta 15
Wcmewm_#u!@zMF$V@AgKvR~i5_Q3eeF
delta 15
Wcmewm_#u!@zMF%gXwOErR~i5`P6jdn
diff --git a/tools/cutadapt/test-data/cutadapt_trimmed.out.gz b/tools/cutadapt/test-data/cutadapt_trimmed.out.gz
index 33196cc42ab29a21434fee896e5fe41cc4f615d3..de11bd1355e2bb671fbadc535776a03b384c59f0 100644
GIT binary patch
delta 15
WcmbQqGLwZ(zMF$#>8*`y!b|`n>;ygl
delta 15
WcmbQqGLwZ(zMF&L!|si2!b|`p69j4i
diff --git a/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz b/tools/cutadapt/test-data/cutadapt_untrimmed.out.gz
index 6a54f5bfb7adf9f600211ca823ed1e2d7e0e2335..17f6112267b603f6773fe4166f195f42b8dd9995 100644
GIT binary patch
delta 15
WcmdlVw?B?ezMF$#>8*`ymihoNu?3L;
delta 15
WcmdlVw?B?ezMF&L!|si2mihoO*af`+
diff --git a/tools/cutadapt/test-data/unknown.fastq.gz b/tools/cutadapt/test-data/unknown.fastq.gz
index 6741330278cdf0f82b13df1aea4565f1b7921986..20ca13409723ca431d9bd1e88dba4adf37529801 100644
GIT binary patch
delta 14
VcmZ3>xR#MkzMF%g{MJOa<p3YN1f&1}
delta 14
VcmZ3>xR#MkzMF&L$nJ@3%K;$41kwNi
From 005022d4218e0393421544fdb945b57ab3d7ffcb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Wed, 2 Jun 2021 21:40:50 +0200
Subject: [PATCH 16/20] Update test rename
---
tools/cutadapt/cutadapt.xml | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index f928a804f86..c6db18de2dd 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -631,14 +631,13 @@ $read_mod_options.zero_cap
<param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
<param name="adapter_source_list" value="user"/>
<param name="adapter" value="AGATCGGAAGAGC"/>
- <param name="adapter_name" value="test_adapter"/>
<section name="read_mod_options">
<param name="cut" value="5"/>
<param name="rename" value="{id} barcode={cut_prefix}"/>
</section>
<output name="out1" file="cutadapt_small_rename.out" ftype="fastq">
<assert_contents>
- <has_line line="@prefix:1_13_573/1 barcode=CGTCCGAANT"/>
+ <has_text text="@prefix:1_13_573/1 barcode=AGCTA"/>
</assert_contents>
</output>
</test>
From d91680ef8d475f4585fe8fdff690dd07d479524b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Wed, 2 Jun 2021 22:00:44 +0200
Subject: [PATCH 17/20] Fix test rename
---
tools/cutadapt/cutadapt.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index c6db18de2dd..0aad5847ea9 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -637,7 +637,7 @@ $read_mod_options.zero_cap
</section>
<output name="out1" file="cutadapt_small_rename.out" ftype="fastq">
<assert_contents>
- <has_text text="@prefix:1_13_573/1 barcode=AGCTA"/>
+ <has_text text="@prefix:1_13_1259/1 barcode=AGCCG"/>
</assert_contents>
</output>
</test>
From d5bf5cc44e9d3ac0268c2e90aad4ffc5ed48d042 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Wed, 2 Jun 2021 22:14:23 +0200
Subject: [PATCH 18/20] Update adapter internal paired reads
---
tools/cutadapt/macros.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tools/cutadapt/macros.xml b/tools/cutadapt/macros.xml
index a6d71a25055..f7324f01288 100644
--- a/tools/cutadapt/macros.xml
+++ b/tools/cutadapt/macros.xml
@@ -117,7 +117,7 @@
#end for
#for $fa in $library.r2.front_adapters2
#if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
- -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2.fields.name}'='${fa.front_adapter_source2.front_adapter2}'
+ -G '${fa.front_adapter_source2.front_adapter2.fields.name}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
#else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
-G file:'${adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}'
#else if str($fa.front_adapter_source2.front_adapter_name2) != "":
From 755b7c3e1ae27e2bcdd540cb04788ef8826af050 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Wed, 2 Jun 2021 23:58:14 +0200
Subject: [PATCH 19/20] Modify max and min length format
---
tools/cutadapt/cutadapt.xml | 150 ++++++++++++++----
tools/cutadapt/test-data/A1.fastq.gz | Bin 340 -> 340 bytes
tools/cutadapt/test-data/A2.fastq.gz | Bin 326 -> 326 bytes
.../test-data/cutadapt_nextseq_out.fq.gz | Bin 12158 -> 12158 bytes
.../cutadapt_out1_internal_adapter.fq.gz | Bin 12180 -> 12180 bytes
.../test-data/cutadapt_out1_max_length.fq.gz | Bin 134 -> 134 bytes
.../test-data/cutadapt_out1_max_min_01.fq.gz | Bin 0 -> 134 bytes
.../test-data/cutadapt_out1_max_min_02.fq.gz | Bin 0 -> 134 bytes
.../test-data/cutadapt_out1_min_length.fq.gz | Bin 9298 -> 9298 bytes
.../cutadapt_out2_internal_adapter.fq.gz | Bin 12153 -> 12153 bytes
.../test-data/cutadapt_out2_max_length.fq.gz | Bin 139 -> 139 bytes
.../test-data/cutadapt_out2_max_min_01.fq.gz | Bin 0 -> 139 bytes
.../test-data/cutadapt_out2_max_min_02.fq.gz | Bin 0 -> 139 bytes
.../test-data/cutadapt_out2_min_length.fq.gz | Bin 10480 -> 10480 bytes
.../test-data/cutadapt_trimmed.out.gz | Bin 537 -> 537 bytes
.../test-data/cutadapt_untrimmed.out.gz | Bin 12095 -> 12095 bytes
tools/cutadapt/test-data/unknown.fastq.gz | Bin 173 -> 173 bytes
17 files changed, 120 insertions(+), 30 deletions(-)
create mode 100644 tools/cutadapt/test-data/cutadapt_out1_max_min_01.fq.gz
create mode 100644 tools/cutadapt/test-data/cutadapt_out1_max_min_02.fq.gz
create mode 100644 tools/cutadapt/test-data/cutadapt_out2_max_min_01.fq.gz
create mode 100644 tools/cutadapt/test-data/cutadapt_out2_max_min_02.fq.gz
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 0aad5847ea9..4dc2ac6d882 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -1,5 +1,5 @@
<tool id="cutadapt" name="Cutadapt" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
- <description>Remove adapter sequences from Fastq/Fasta</description>
+ <description>Remove adapter sequences from FASTQ/FASTA</description>
<macros>
<import>macros.xml</import>
</macros>
@@ -109,14 +109,14 @@ $adapter_options.revcomp
$filter_options.discard_trimmed
$filter_options.discard_untrimmed
-#if str($filter_options.minimum_options.minimum_r2) == 'True':
- --minimum-length=$filter_options.minimum_length:$filter_options.minimum_options.value_minimum
-#elif str($filter_options.minimum_length):
+#if str($filter_options.minimum_length) and str($filter_options.length_R2_options.length_R2_status) == 'True':
+ --minimum-length=$filter_options.minimum_length:$filter_options.length_R2_options.R2_minimum
+#else if str($filter_options.minimum_length):
--minimum-length=$filter_options.minimum_length
#end if
-#if str($filter_options.maximum_options.maximum_r2) == 'True':
- --maximum-length=$filter_options.maximum_length:$filter_options.maximum_options.value_maximum
-#elif str($filter_options.maximum_length):
+#if str($filter_options.maximum_length) and str($filter_options.length_R2_options.length_R2_status) == 'True':
+ --maximum-length=$filter_options.maximum_length:$filter_options.length_R2_options.R2_maximum
+#else if str($filter_options.maximum_length):
--maximum-length=$filter_options.maximum_length
#end if
#if str($filter_options.max_n):
@@ -224,30 +224,20 @@ $read_mod_options.zero_cap
<section name="filter_options" title="Filter Options">
<param argument="--discard-trimmed" type="boolean" value="False" truevalue="--discard-trimmed" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />
<param argument="--discard_untrimmed" type="boolean" value="False" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." />
- <param argument="--minimum-length" type="integer" min="0" optional="True" value="" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
- <conditional name="minimum_options">
- <param name="minimum_r2" type="select" label="Specify a minimum length for reverse reads (R2)" help="When trimming paired-end reads, the minimum lengths for R1 and R2 can be specified separately. If not provided, the same minimum length applies to both reads.">
+ <param argument="--minimum-length" type="integer" min="0" optional="True" value="" label="Minimum length (R1)" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded." />
+ <param argument="--maximum-length" type="integer" min="0" optional="True" value="" label="Maximum length (R1)" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded." />
+ <conditional name="length_R2_options">
+ <param name="length_R2_status" type="select" label="Specify a minimum/maximum length for reverse reads (R2)" help="When trimming paired-end reads, the minimum/maximum lengths for R1 and R2 can be specified separately. If not provided, the same minimum length applies to both reads.">
<option value="True">Enabled</option>
<option value="False" selected="True">Disabled</option>
</param>
<when value="True">
- <param name="value_minimum" type="integer" min="0" optional="True" value="" label="Minimum length" />
+ <param name="R2_minimum" type="integer" min="0" value="" optional="True" label="Minimum length (R2)" />
+ <param name="R2_maximum" type="integer" min="0" value="" optional="True" label="Maximum length (R2)" />
</when>
<when value="False">
</when>
- </conditional>
- <param argument="--maximum-length" type="integer" min="0" optional="True" value="" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
- <conditional name="maximum_options">
- <param name="maximum_r2" type="select" label="Specify a maximum length for reverse reads (R2)" help="When trimming paired-end reads, the maximum lengths for R1 and R2 can be specified separately. If not provided, the same maximum length applies to both reads.">
- <option value="True">Enabled</option>
- <option value="False" selected="True">Disabled</option>
- </param>
- <when value="True">
- <param name="value_maximum" type="integer" min="0" optional="True" value="" label="Maximum length" />
- </when>
- <when value="False">
- </when>
- </conditional>
+ </conditional>
<param argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
<param argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
<option value="any" selected="True">Any: a read pair is discarded (or redirected) if one of the reads (R1 or R2) fulfills the filtering criterion. </option>
@@ -705,9 +695,9 @@ $read_mod_options.zero_cap
<section name="filter_options">
<param name="minimum_length" value="30"/>
<param name="pair_filter" value="both"/>
- <conditional name="minimum_options">
- <param name="minimum_r2" value="True"/>
- <param name="value_minimum" value="10"/>
+ <conditional name="length_R2_options">
+ <param name="length_R2_status" value="True"/>
+ <param name="R2_minimum" value="10"/>
</conditional>
</section>
<output name="out1" decompress="True" file="cutadapt_out1_min_length.fq.gz" ftype="fastq.gz"/>
@@ -729,9 +719,9 @@ $read_mod_options.zero_cap
<section name="filter_options">
<param name="pair_filter" value="both"/>
<param name="maximum_length" value="50"/>
- <conditional name="maximum_options">
- <param name="maximum_r2" value="True"/>
- <param name="value_maximum" value="30"/>
+ <conditional name="length_R2_options">
+ <param name="length_R2_status" value="True"/>
+ <param name="R2_maximum" value="30"/>
</conditional>
</section>
<output name="out1" decompress="True" file="cutadapt_out1_max_length.fq.gz" ftype="fastq.gz"/>
@@ -741,6 +731,106 @@ $read_mod_options.zero_cap
<has_text text="--pair-filter=both"/>
</assert_command>
</test>
+ <!-- Test combination maximum and minimum length paired reads -->
+ <test expect_num_outputs="2">
+ <param name="type" value="paired" />
+ <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
+ <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="adapter_source_list2" value="user"/>
+ <param name="adapter2" value="AGATCGGAAGAGC"/>
+ <section name="filter_options">
+ <param name="pair_filter" value="both"/>
+ <param name="minimum_length" value="10"/>
+ <param name="maximum_length" value="50"/>
+ <conditional name="length_R2_options">
+ <param name="length_R2_status" value="True"/>
+ <param name="R2_maximum" value="30"/>
+ </conditional>
+ </section>
+ <output name="out1" decompress="True" file="cutadapt_out1_max_min_01.fq.gz" ftype="fastq.gz"/>
+ <output name="out2" decompress="True" file="cutadapt_out2_max_min_01.fq.gz" ftype="fastq.gz"/>
+ <assert_command>
+ <has_text text="--minimum-length=10:"/>
+ <has_text text="--maximum-length=50:30"/>
+ <has_text text="--pair-filter=both"/>
+ </assert_command>
+ </test>
+ <test expect_num_outputs="2">
+ <param name="type" value="paired" />
+ <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
+ <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="adapter_source_list2" value="user"/>
+ <param name="adapter2" value="AGATCGGAAGAGC"/>
+ <section name="filter_options">
+ <param name="pair_filter" value="both"/>
+ <param name="minimum_length" value="10"/>
+ <param name="maximum_length" value="50"/>
+ <conditional name="length_R2_options">
+ <param name="length_R2_status" value="True"/>
+ <param name="R2_minimum" value="10"/>
+ </conditional>
+ </section>
+ <output name="out1" decompress="True" file="cutadapt_out1_max_min_02.fq.gz" ftype="fastq.gz"/>
+ <output name="out2" decompress="True" file="cutadapt_out2_max_min_02.fq.gz" ftype="fastq.gz"/>
+ <assert_command>
+ <has_text text="--minimum-length=10:10"/>
+ <has_text text="--maximum-length=50:"/>
+ <has_text text="--pair-filter=both"/>
+ </assert_command>
+ </test>
+ <test expect_num_outputs="2">
+ <param name="type" value="paired" />
+ <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
+ <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="adapter_source_list2" value="user"/>
+ <param name="adapter2" value="AGATCGGAAGAGC"/>
+ <section name="filter_options">
+ <param name="pair_filter" value="both"/>
+ <conditional name="length_R2_options">
+ <param name="length_R2_status" value="True"/>
+ <param name="R2_minimum" value="10"/>
+ <param name="R2_maximum" value="50"/>
+ </conditional>
+ </section>
+ <output name="out1" decompress="True" file="cutadapt_out1_max_min_03.fq.gz" ftype="fastq.gz"/>
+ <output name="out2" decompress="True" file="cutadapt_out2_max_min_03.fq.gz" ftype="fastq.gz"/>
+ <assert_command>
+ <has_text text="--minimum-length=:10"/>
+ <has_text text="--maximum-length=:50"/>
+ <has_text text="--pair-filter=both"/>
+ </assert_command>
+ </test>
+ <test expect_num_outputs="2">
+ <param name="type" value="paired" />
+ <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
+ <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
+ <param name="adapter_source_list" value="user"/>
+ <param name="adapter" value="AGATCGGAAGAGC"/>
+ <param name="adapter_source_list2" value="user"/>
+ <param name="adapter2" value="AGATCGGAAGAGC"/>
+ <section name="filter_options">
+ <param name="minimum_length" value="10"/>
+ <param name="pair_filter" value="both"/>
+ <conditional name="length_R2_options">
+ <param name="length_R2_status" value="True"/>
+ <param name="R2_minimum" value="10"/>
+ <param name="R2_maximum" value="40"/>
+ </conditional>
+ </section>
+ <output name="out1" decompress="True" file="cutadapt_out1_max_min_04.fq.gz" ftype="fastq.gz"/>
+ <output name="out2" decompress="True" file="cutadapt_out2_max_min_04.fq.gz" ftype="fastq.gz"/>
+ <assert_command>
+ <has_text text="--minimum-length=10:10"/>
+ <has_text text="--maximum-length=:40"/>
+ <has_text text="--pair-filter=both"/>
+ </assert_command>
+ </test>
<!-- Test length options -->
<test expect_num_outputs="1">
<param name="type" value="single" />
diff --git a/tools/cutadapt/test-data/A1.fastq.gz b/tools/cutadapt/test-data/A1.fastq.gz
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From fae23a9dbf4ae8a25c6d0e466181facf4f099006 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
<gallardo@informatik.uni-freiburg.de>
Date: Thu, 3 Jun 2021 00:03:45 +0200
Subject: [PATCH 20/20] Remove test 3 combination max and min length
---
tools/cutadapt/cutadapt.xml | 49 -------------------------------------
1 file changed, 49 deletions(-)
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 4dc2ac6d882..cadeeb1a889 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -782,55 +782,6 @@ $read_mod_options.zero_cap
<has_text text="--pair-filter=both"/>
</assert_command>
</test>
- <test expect_num_outputs="2">
- <param name="type" value="paired" />
- <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
- <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
- <param name="adapter_source_list" value="user"/>
- <param name="adapter" value="AGATCGGAAGAGC"/>
- <param name="adapter_source_list2" value="user"/>
- <param name="adapter2" value="AGATCGGAAGAGC"/>
- <section name="filter_options">
- <param name="pair_filter" value="both"/>
- <conditional name="length_R2_options">
- <param name="length_R2_status" value="True"/>
- <param name="R2_minimum" value="10"/>
- <param name="R2_maximum" value="50"/>
- </conditional>
- </section>
- <output name="out1" decompress="True" file="cutadapt_out1_max_min_03.fq.gz" ftype="fastq.gz"/>
- <output name="out2" decompress="True" file="cutadapt_out2_max_min_03.fq.gz" ftype="fastq.gz"/>
- <assert_command>
- <has_text text="--minimum-length=:10"/>
- <has_text text="--maximum-length=:50"/>
- <has_text text="--pair-filter=both"/>
- </assert_command>
- </test>
- <test expect_num_outputs="2">
- <param name="type" value="paired" />
- <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
- <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
- <param name="adapter_source_list" value="user"/>
- <param name="adapter" value="AGATCGGAAGAGC"/>
- <param name="adapter_source_list2" value="user"/>
- <param name="adapter2" value="AGATCGGAAGAGC"/>
- <section name="filter_options">
- <param name="minimum_length" value="10"/>
- <param name="pair_filter" value="both"/>
- <conditional name="length_R2_options">
- <param name="length_R2_status" value="True"/>
- <param name="R2_minimum" value="10"/>
- <param name="R2_maximum" value="40"/>
- </conditional>
- </section>
- <output name="out1" decompress="True" file="cutadapt_out1_max_min_04.fq.gz" ftype="fastq.gz"/>
- <output name="out2" decompress="True" file="cutadapt_out2_max_min_04.fq.gz" ftype="fastq.gz"/>
- <assert_command>
- <has_text text="--minimum-length=10:10"/>
- <has_text text="--maximum-length=:40"/>
- <has_text text="--pair-filter=both"/>
- </assert_command>
- </test>
<!-- Test length options -->
<test expect_num_outputs="1">
<param name="type" value="single" />