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Fix 2 bugs in SRST2 #6493

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merged 4 commits into from
Oct 28, 2024
Merged

Fix 2 bugs in SRST2 #6493

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95537f2
Separate gene typing reports
hexylena Oct 28, 2024
d700148
Fixes https://github.com/galaxyproject/tools-iuc/issues/6487
hexylena Oct 28, 2024
b400dd9
bump galaxy version
hexylena Oct 28, 2024
8402025
correct output number
hexylena Oct 28, 2024
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2 changes: 1 addition & 1 deletion tools/srst2/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">0.2.0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
<token name="@PROFILE@">20.01</token>
<xml name="requirements">
<requirements>
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20 changes: 14 additions & 6 deletions tools/srst2/srst2.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -103,9 +103,11 @@ srst2
#if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes"
&& mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput | true
#end if

#if $use_gene_db.selector == "yes" and $use_gene_db.no_gene_details
&& mkdir -p geneTypingOutput/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutput | true
&& mkdir -p geneTypingOutput/ geneTypingOutputFull/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutputFull | true
#end if

#if 'save_scores' in str($output_files_selector)
&& mkdir -p scoresOutput/ && cp *.scores scoresOutput | true
#end if
Expand Down Expand Up @@ -154,7 +156,7 @@ srst2
<add value="_" />
</valid>
</sanitizer>
<validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
<validator type="regex">[A-Za-z0-9 =_/+-]+</validator>
</param>
<param argument="--mlst_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for MLST allele calling"/>
<param argument="--min_depth" type="integer" value="5" label="Minimum mean depth to flag as dubious allele call"/>
Expand Down Expand Up @@ -198,7 +200,11 @@ srst2
<filter>use_mlst_db['selector'] == "yes"</filter>
</data>
<collection name="gene_typing" type="list" label="${tool.name} on ${on_string}: Gene typing results files" >
<discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="txt,tabular"/>
<discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="tabular"/>
<filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
</collection>
<collection name="gene_typing_full" type="list" label="${tool.name} on ${on_string}: Full Gene typing results files" >
<discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutputFull" format="tabular"/>
<filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
</collection>
<data name="Compiled_gene_and_mlst_output" format="tabular" from_work_dir="output__compiledResults.txt" label="${tool.name} on ${on_string}: Compiled MLST and Gene databases Results">
Expand Down Expand Up @@ -227,7 +233,7 @@ srst2
</data>
</outputs>
<tests>
<test expect_num_outputs="9">
<test expect_num_outputs="10">
<param name="prob_err" value="0.01"/>
<param name="max_unaligned_overlap" value="10"/>
<param name="mapq" value="1"/>
Expand Down Expand Up @@ -264,13 +270,15 @@ srst2
</assert_contents>
</output>
<output_collection name="gene_typing" type="list">
<element name="output__fullgenes__0-gene_db__results.txt">
<element name="output__genes__0-gene_db__results.txt">
<assert_contents>
<has_text text="AmpC1_Ecoli_Bla"/>
<has_n_lines n="2"/>
</assert_contents>
</element>
<element name="output__genes__0-gene_db__results.txt">
</output_collection>
<output_collection name="gene_typing_full" type="list">
<element name="output__fullgenes__0-gene_db__results.txt">
<assert_contents>
<has_text text="AmpC1_Ecoli_Bla"/>
<has_n_lines n="2"/>
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