Mercurial > repos > iuc > cooc_tabmut
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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 13:50:09 +0000 |
parents | |
children | 579538ff939d |
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<tool id="cooc_tabmut" name="Cojac: tabmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> export cooccurrence mutations as a table </description> <macros> <import>macros.xml</import> </macros> <expand macro="biotools"/> <expand macro="requirements"/> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ #for $input_file in $cooc_file #set $cooc_ext = $input_file.ext #end for cooc-tabmut #if $cooc_ext == 'json' -j '$cooc_file' #else if $cooc_ext == 'yaml' -y '$cooc_file' #end if -o cooc-table.csv #if $table_orientation.choice == 'lines' -l #else if $table_orientation.choice == 'multiindex' -m #end if -q ]]></command> <inputs> <param name="cooc_file" type="data" format="json,yaml" multiple="true" label="Results generated by mutbamscan"/> <conditional name="table_orientation"> <param name="choice" type="select" label="Output table orientation"> <option value="columns">Column-oriented table (default)</option> <option value="lines">Line-oriented table</option> <option value="multiindex">Multi-level indexing (amplicons and counts categories) </option> </param> <when value="columns"/> <when value="lines"/> <when value="multiindex"/> </conditional> </inputs> <outputs> <data name="table" format="csv" label="${tool.name} on ${on_string}: Mutation cooccurrence (CSV table)" from_work_dir="cooc-table.csv"> </data> </outputs> <tests> <test expect_num_outputs="1"> <param name="cooc_file" value="cooc-test111.json"/> <conditional name="table_orientation"> <param name="choice" value="columns"/> </conditional> <output name="table" ftype="csv"> <assert_contents> <has_text text="A76_om1.count"/> <has_text text="A76_om1.mut_oneless"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ @HELP_HEADER@ Information about **cooc_tabmut** method ======================================== The method exports a JSON or YAML file as a CSV/TSV table for downstream analysis (e.g.: RStudio). ]]></help> <expand macro="citations"/> </tool>