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das tool: do not allow empty labels #5955

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Apr 29, 2024
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das tool: do not allow empty labels #5955

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das tool: do not allow empty labels
bernt-matthias Apr 16, 2024
2cb5a29
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bernt-matthias Apr 24, 2024
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75 changes: 68 additions & 7 deletions tools/das_tool/das_tool.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,19 +7,26 @@
<expand macro="requirements"/>
<expand macro="version"/>
<command detect_errors="exit_code"><![CDATA[
#set $bins = ""
#set $labels = ""
#set $sep = ""
#import re

#set $bins = []
#set $labels = []
#for $i, $s in enumerate($binning)
#set $bins += "%s%s" %($sep, $s.bins)
#set $labels += "%s%s" %($sep, $s.labels)
#set $sep = ","
#silent $bins.append(str($s.bins))
#if $s.labels != ''
#silent $labels.append(str($s.labels))
#else
#silent $labels.append(re.sub('[^\w\-_\.]', '_', $s.bins.element_identifier))
#end if
#end for

#if $adv.proteins
ln -s '$adv.proteins' 'proteins' &&
#end if

#set $bins = ','.join($bins)
#set $labels = ','.join($labels)

DAS_Tool
--contigs '$contigs'
--outputbasename 'outputs'
Expand All @@ -46,7 +53,15 @@ DAS_Tool
<param argument="--contigs" type="data" format="fasta" label="Contig sequences"/>
<repeat name="binning" title="Bins" min="1">
<param argument="--bins" type="data" format="tabular" label="Contigs-to-bin table" help="Tabular with two columns: contig-IDs and bin-IDs. Fasta_to_Contigs2Bin can be used to Converts genome bins in fasta format to Contigs-to-bin table"/>
<param argument="--labels" type="text" value="" label="Name of binning prediction tool used to generate the table"/>
<param argument="--labels" type="text" value="" label="Name of binning prediction name" help="If left empty the identifier of the contig-to-bin table is used. Only alphanumeric characters, dash, underscore and dor are allowed. Other characters are replaced by underscore.">
<sanitizer invalid_char="_">
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_ is invalid and then you add it again?

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invalid_char specifies the character used as a replacement for invalid characters. _ is a valid char.

Idea is that this does the same as the regexp that is applied to the element_identifiers in the cheetah code (which I took from what we use all the time).

<valid initial="string.ascii_letters,string.digits">
<add value="-" />
<add value="_" />
<add value="." />
</valid>
</sanitizer>
</param>
</repeat>
<section name="adv" title="Advanced options">
<param argument="--search_engine" type="select" label="Engine used for single copy gene identification">
Expand Down Expand Up @@ -139,6 +154,52 @@ DAS_Tool
</assert_contents>
</output>
</test>
<!-- like the first test, but with empty label -->
<test expect_num_outputs="4">
<param name="contigs" value="contigs.fasta"/>
<repeat name="binning">
<param name="bins" value="metabat.tabular"/>
<!-- <param name="labels" value="metabat"/> -->
</repeat>
<section name="adv">
<param name="search_engine" value="diamond"/>
<param name="proteins" value="proteins.fasta"/>
<param name="score_threshold" value="0.5"/>
<param name="duplicate_penalty" value="0.6"/>
<param name="megabin_penalty" value="0.5" />
</section>
<section name="output">
<param name="write_bin_evals" value="true"/>
<conditional name="write_bins">
<param name="write_bins" value=""/>
</conditional>
<param name="debug" value="true"/>
</section>
<output name="summary" ftype="tabular">
<assert_contents>
<has_text text="unique_SCGs"/>
<has_text text="metabat.8"/>
<has_text text="bacteria"/>
</assert_contents>
</output>
<output name="contigs2bin" ftype="tabular">
<assert_contents>
<has_text text="Ley3_66761_scaffold_6"/>
</assert_contents>
</output>
<output name="log" ftype="txt">
<assert_contents>
<has_text text="Skipping gene prediction"/>
<has_text text="#Target sequences to report alignments for: 1"/>
</assert_contents>
</output>
<output name="eval" ftype="tabular">
<assert_contents>
<has_text text="unique_SCGs"/>
<has_text text="metabat.8"/>
</assert_contents>
</output>
</test>
<test expect_num_outputs="6">
<param name="contigs" value="contigs.fasta"/>
<repeat name="binning">
Expand Down
6 changes: 3 additions & 3 deletions tools/das_tool/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">1.1.7</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">21.01</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">22.01</token>
<xml name="biotools">
<xrefs>
<xref type="bio.tools">dastool</xref>
Expand All @@ -28,4 +28,4 @@ DAS Tool is an automated method that integrates the results of a flexible number
<citation type="doi">10.1038/s41564-018-0171-1</citation>
</citations>
</xml>
</macros>
</macros>