Mercurial > repos > iuc > humann_split_table
view humann_genefamilies_genus_level @ 3:cc6a10100a14 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 32d4c566afe55179531fdd106dc5a996cc09bbb1
author | iuc |
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date | Wed, 29 Mar 2023 20:01:50 +0000 |
parents | 506d4a349aa1 |
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<!-- The tool is broken with current version of HUMAnN. Once it will be fixed (PR merged), we can update this wrapper and add the XML extension to enable it --> <tool id="humann_genefamilies_genus_level" name="Create a genus level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>gene families and pathways from HUMAnN species level gene families</description> <macros> <import>macros.xml</import> </macros> <expand macro="edam_ontology"/> <expand macro="requirements"/> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ humann_genefamilies_genus_level --input '$input' --output '$gene_families' && humann --input '$gene_families' --output '$pathways' ]]></command> <inputs> <param argument="--input" type="data" format="tsv,tabular" label="Species level gene families" help="Direct output from HUMAnN"/> </inputs> <outputs> <data name="gene_families" format="tabular" label="${tool.name} on ${on_string}: Genus level gene families"/> <data name="pathways" format="tabular" label="${tool.name} on ${on_string}: Genus level pathways"/> </outputs> <tests> <test expect_num_outputs="1"> <param name="input" value="demo_genefamilies.tsv"/> <output name="gene_families" ftype="tabular" value="genus-level-gene-families.tsv" compare="sim_size"> <assert_contents> <has_text text="humann_Abundance"/> <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/> <has_n_columns n="2"/> </assert_contents> </output> <output name="pathways" ftype="tabular" value="genus-level-pathways.tsv" compare="sim_size"> <assert_contents> <has_text text="humann_Abundance"/> <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/> <has_n_columns n="2"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ @HELP_HEADER@ By default, the gene families and pathways output files from HUMAnN are species level. This tool generates genus level gene families and pathways ]]></help> <expand macro="citations"/> </tool>