Mercurial > repos > iuc > cooc_mutbamscan
view cooc_mutbamscan.xml @ 0:373c1735d31f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
author | iuc |
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date | Thu, 11 Aug 2022 13:50:37 +0000 |
parents | |
children | 9f1660129403 |
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<tool id="cooc_mutbamscan" name="Cojac: mutbamscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> scan an alignment file for mutation co-occurrences </description> <macros> <import>macros.xml</import> </macros> <expand macro="biotools"/> <expand macro="requirements"/> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ ln -s '$bed_file' 'bed_file' && @VOCDIR_COMMAND@ #import re #set identifier = re.sub('[^\s\w\-\\.]', '_', str($bam_file.element_identifier)) ln -s '$bam_file' ${identifier}.bam && ln -s '${bam_file.metadata.bam_index}' ${identifier}.bai && cooc-mutbamscan -a '${identifier}.bam' -b 'bed_file' -m '$vocdir' -y cooc.yaml -j cooc.json #if $amplicons_file.choice == 'build' -A amplicons.yaml #else -Q '$amplicons_file.in_amp' #end if -t cooc.tsv --cooc $cooc ]]></command> <inputs> <expand macro="vocdir_input"/> <param name="bed_file" type="data" format="bed" label="BED file defining the amplicons"/> <param name="bam_file" type="data" format="bam,cram,sam" label="Alignment BAM/CRAM/SAM file"/> <param argument="--cooc" type="integer" min="1" value="2" label="Minimum number of cooccurence mutations on the same amplicon"/> <conditional name="amplicons_file"> <param name="choice" type="select" label="Source of amplicons YAML file"> <option value="build">Build from BED + set of YAMLs for variants of concern</option> <option value="custom">From history</option> </param> <when value="build"/> <when value="custom"> <param name="in_amp" type="data" format="yaml" label="YAML file to query amplicons"/> </when> </conditional> <param name="output_files" type="select" display="checkboxes" multiple="true" label="Output files"> <option value="yaml" selected="true">YAML</option> <option value="json">JSON</option> <option value="tabular">tabular</option> </param> </inputs> <outputs> <data name="cooc_yaml" format="yaml" label="${tool.name} on ${on_string}: Mutation cooccurrence (yaml)" from_work_dir="cooc.yaml"> <filter>'yaml' in output_files</filter> </data> <data name="cooc_json" format="json" label="${tool.name} on ${on_string}: Mutation cooccurrence (json)" from_work_dir="cooc.json"> <filter>'json' in output_files</filter> </data> <data name="cooc_tsv" format="tabular" label="${tool.name} on ${on_string}: Mutation cooccurrence (tabular)" from_work_dir="cooc.tsv"> <filter>'tabular' in output_files</filter> </data> <data name="amplicons" format="yaml" label="${tool.name} on ${on_string}: Amplicons (yaml)" from_work_dir="amplicons.yaml"> <filter>amplicons_file['choice'] == 'build'</filter> </data> </outputs> <tests> <!-- Test 1: build yaml for amplicons from bed and voc/ --> <test expect_num_outputs="4"> <conditional name="vocdir_option"> <param name="choice" value="custom"/> <param name="voc_file" value="omicron_ba1_mutations.yaml"/> </conditional> <param name="bam_file" value="tbam11.bam"/> <param name="bed_file" value="nCoV-2019.insert.V3.bed"/> <conditional name="amplicons_file"> <param name="choice" value="build"/> </conditional> <param name="output_files" value="yaml,json,tabular"/> <output name="cooc_yaml" ftype="yaml"> <assert_contents> <has_text text="76_om1"/> <has_text text="81_om1"/> </assert_contents> </output> <output name="cooc_json" ftype="json"> <assert_contents> <has_text text="76_om1"/> <has_text text="81_om1"/> </assert_contents> </output> <output name="cooc_tsv" ftype="tabular"> <assert_contents> <has_text text="76_om1"/> <has_text text="81_om1"/> </assert_contents> </output> <output name="amplicons" ftype="yaml"> <assert_contents> <has_text text="76_om1"/> <has_text text="81_om1"/> </assert_contents> </output> </test> <!-- Test 2: supply yaml for amplicons and voc/ from cache --> <test expect_num_outputs="2"> <conditional name="vocdir_option"> <param name="choice" value="cache"/> </conditional> <param name="bam_file" value="tbam11.bam"/> <param name="bed_file" value="nCoV-2019.insert.V3.bed"/> <conditional name="amplicons_file"> <param name="choice" value="custom"/> <param name="in_amp" value="amplicons111.yaml"/> </conditional> <param name="output_files" value="yaml,tabular"/> <output name="cooc_yaml" ftype="yaml"> <assert_contents> <has_text text="76_om1"/> <has_text text="81_om1"/> </assert_contents> </output> <output name="cooc_tsv" ftype="tabular"> <assert_contents> <has_text text="76_om1"/> <has_text text="81_om1"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ @HELP_HEADER@ Information about **cooc-mutbamscan** method ============================================ The method scans an alignment BAM/CRAM/SAM file for mutation co-occurrences and output a JSON or YAML file. ]]></help> <expand macro="citations"/> </tool>