Mercurial > repos > iuc > humann_join_tables
view humann_join_tables.xml @ 4:a060a76c3a13 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0a3abeca0535457ddf39c394001d61cd2e45afdd
author | iuc |
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date | Mon, 24 Apr 2023 18:54:35 +0000 |
parents | cf7f80d59099 |
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<tool id="humann_join_tables" name="Join (merge)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table</description> <macros> <import>macros.xml</import> </macros> <expand macro="edam_ontology"/> <expand macro="requirements"/> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ #import re mkdir tmp_dir && #for $input in $inputs ln -s '$input' 'tmp_dir/${re.sub('[^\w\-_.]', '_', input.element_identifier)}' && #end for humann_join_tables -i 'tmp_dir' -o '$output' ]]></command> <inputs> <param name="inputs" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table"/> </inputs> <outputs> <data format="tabular" name="output"/> </outputs> <tests> <test expect_num_outputs="1"> <param name="inputs" value="demo_pathabundance.tsv,demo_pathcoverage.tsv"/> <output name="output" ftype="tabular" value="demo_joined_pathabundance_pathcoverage.tsv"> <assert_contents> <has_text text="humann_Abundance" /> <has_text text="humann_Coverage" /> <has_text text="UNINTEGRATED|unclassified" /> <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ @HELP_HEADER@ This tool joins (merges) multiple single-sample output files into a single table with multiple samples. It can also be used to join multiple multi-sample output files into a single table. ]]></help> <expand macro="citations"/> </tool>