Mercurial > repos > iuc > cooc_tabmut
diff cooc_tabmut.xml @ 0:4be399803856 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 13:50:09 +0000 |
parents | |
children | 579538ff939d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cooc_tabmut.xml Thu Aug 11 13:50:09 2022 +0000 @@ -0,0 +1,76 @@ +<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>