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ivar upgrade and add primer_scheme_bedfiles support #2979

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merged 7 commits into from
Apr 22, 2020
Merged

ivar upgrade and add primer_scheme_bedfiles support #2979

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d938d28
Merge branch 'master' of https://github.com/galaxyproject/tools-iuc
pvanheus Apr 19, 2020
ec88f27
Merge branch 'master' of https://github.com/galaxyproject/tools-iuc
pvanheus Apr 21, 2020
faa9de3
Bump version, add data manager support
pvanheus Apr 21, 2020
50a5dfc
Change label for cached_bed
pvanheus Apr 21, 2020
5a8b670
Add test for cached BED
pvanheus Apr 22, 2020
74475dd
Put tabs instead of spaces in .loc file
pvanheus Apr 22, 2020
38189dd
Rename ARTIC to SARS-CoV-2-ARTIC
pvanheus Apr 22, 2020
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42 changes: 38 additions & 4 deletions tools/ivar/ivar_trim.xml
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Expand Up @@ -6,7 +6,11 @@
<expand macro="requirements" />
<expand macro="version_command" />
<command detect_errors="exit_code"><![CDATA[
ln -s '$input_bed' bed.bed &&
#if $primer.source == "history"
ln -s '$primer.input_bed' bed.bed &&
#else
ln -s '$primer.cached_bed.fields.path' bed.bed &&
#end if
ln -s '$input_bam' sorted.bam &&
ivar trim
-i sorted.bam
Expand All @@ -21,7 +25,23 @@
]]> </command>
<inputs>
<param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
<param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
<conditional name="primer">
<param label="Source of primer information" name="source" type="select">
<option value="history" selected="true">History</option>
<option value="cached">Built-in</option>
</param>
<when value="history">
<param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
</when>
<when value="cached">
<param name="cached_bed" type="select" label="Primer scheme name" help="Select primer scheme bed file from a list">
<options from_data_table="primer_scheme_bedfiles">
<filter type="sort_by" column="1" />
<validator type="no_options" message="No primer schemes are available" />
</options>
</param>
</when>
</conditional>
<param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/>
<param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/>
<param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/>
Expand All @@ -40,15 +60,29 @@
</test>
<!-- #1: Zika data-->
<test>
<conditional name="primer">
<param name="source" value="history" />
<param name="input_bed" value="zika/db/zika_primers.bed" />
</conditional>
<param name="input_bam" value="zika/Z52_a.sorted.bam" />
<param name="input_bed" value="zika/db/zika_primers.bed" />
<output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
</test>
<test>
<conditional name="primer">
<param name="source" value="history" />
<param name="input_bed" value="zika/db/zika_primers.bed" />
</conditional>
<param name="input_bam" value="zika/Z52_b.sorted.bam" />
<param name="input_bed" value="zika/db/zika_primers.bed" />
<output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
</test>
<test>
<conditional name="primer">
<param name="source" value="cached" />
<param name="cached_bed" value="SARS-CoV-2-ARTICv1" />
</conditional>
<param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" />
<output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" />
</test>
</tests>
<help><![CDATA[
iVar uses primer positions supplied in a BED file to soft clip primer
Expand Down
2 changes: 1 addition & 1 deletion tools/ivar/macros.xml
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@@ -1,5 +1,5 @@
<macros>
<token name="@VERSION@">1.2</token>
<token name="@VERSION@">1.2.1</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="@VERSION@">ivar</requirement>
Expand Down
8 changes: 8 additions & 0 deletions tools/ivar/test-data/primer_scheme_bedfiles.loc
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# this is a tab separated file describing the location of primer schemes used for amplicon
# sequencing (e.g. using the ARTIC SARS-CoV-2 protocol)
#
# the columns are:
# value description path
#
# for example
SARS-CoV-2-ARTICv1 SARS-CoV-2-ARTIC v1 ${__HERE__}/sars-cov-2/SARS-CoV-2-ARTICv1.bed
196 changes: 196 additions & 0 deletions tools/ivar/test-data/sars-cov-2/SARS-CoV-2-ARTICv1.bed
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8 changes: 8 additions & 0 deletions tools/ivar/tool-data/primer_scheme_bedfiles.loc.sample
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# this is a tab separated file describing the location of primer schemes used for amplicon
# sequencing (e.g. using the ARTIC SARS-CoV-2 protocol)
#
# the columns are:
# value description path
#
# for example
# SARS-CoV-2-ARTICv1 SARS-CoV-2-ARTIC v1 primers /data/galaxy/tool_data/artic_primers/SARS-CoV-2-ARTICv1.bed
7 changes: 7 additions & 0 deletions tools/ivar/tool_data_table_conf.xml.sample
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<tables>
<!-- Locations of primer scheme BED files -->
<table name="primer_scheme_bedfiles" comment_char="#">
<columns>value, description, path</columns>
<file path="tool-data/primer_scheme_bedfiles.loc" />
</table>
</tables>
7 changes: 7 additions & 0 deletions tools/ivar/tool_data_table_conf.xml.test
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<tables>
<!-- Locations of primer scheme BED files -->
<table name="primer_scheme_bedfiles" comment_char="#">
<columns>value, description, path</columns>
<file path="${__HERE__}/test-data/primer_scheme_bedfiles.loc" />
</table>
</tables>