| Previous changeset 2:81cea47ec685 (2024-03-18) |
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Commit message:
planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53 |
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modified:
macros.xml srst2.xml |
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| diff -r 81cea47ec685 -r f995ba9f1caa macros.xml --- a/macros.xml Mon Mar 18 12:32:11 2024 +0000 +++ b/macros.xml Mon Oct 28 13:08:53 2024 +0000 |
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| @@ -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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| diff -r 81cea47ec685 -r f995ba9f1caa srst2.xml --- a/srst2.xml Mon Mar 18 12:32:11 2024 +0000 +++ b/srst2.xml Mon Oct 28 13:08:53 2024 +0000 |
| [ |
| @@ -103,9 +103,11 @@ #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 @@ -154,7 +156,7 @@ <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"/> @@ -198,7 +200,11 @@ <filter>use_mlst_db['selector'] == "yes"</filter> </data> <collection name="gene_typing" type="list" label="${tool.name} on ${on_string}: Gene typing results files" > - <discover_datasets pattern="(?P<designation>.+)" directory="geneTypingOutput" format="txt,tabular"/> + <discover_datasets pattern="(?P<designation>.+)" directory="geneTypingOutput" format="tabular"/> + <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter> + </collection> + <collection name="gene_typing_full" type="list" label="${tool.name} on ${on_string}: Full Gene typing results files" > + <discover_datasets pattern="(?P<designation>.+)" directory="geneTypingOutputFull" format="tabular"/> <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter> </collection> <data name="Compiled_gene_and_mlst_output" format="tabular" from_work_dir="output__compiledResults.txt" label="${tool.name} on ${on_string}: Compiled MLST and Gene databases Results"> @@ -227,7 +233,7 @@ </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"/> @@ -264,13 +270,15 @@ </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"/> |