Mercurial > repos > iuc > picrust_metagenome_contributions
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 899e24f2aecad79c80667fb6c938dd4573a98820
author | iuc |
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date | Fri, 09 Feb 2024 21:42:03 +0000 |
parents | f0f5028a3393 |
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<tool id="picrust_metagenome_contributions" name="Metagenome Contributions" version="@TOOL_VERSION@.0"> <description>of OTUs to user-specified functions</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="aggressive"><![CDATA[ metagenome_contributions.py -i '$input_data' -o '$contrib_table' -c '$gg.precalc' -l '$limit_gene' ]]></command> <inputs> <param name="input_data" type="data" format="biom1,h5" label="Input file" help="Biom file, which should be the output of the normalize_by_copy_number command."/> <expand macro="otu-reference-precalculated"/> <param name="limit_gene" type="text" format="txt" label="Function ids" help="Limit to specified function ids (e.g. K00500). If limiting to multiple ids then separate them by commas with no spaces between them." /> </inputs> <outputs> <data name="contrib_table" format="tabular"/> </outputs> <tests> <test> <param name="input_data" value="otu_table_for_custom_trait_table.biom"/> <param name="source" value="hist"/> <param name="precalc" value="custom_trait_table.tab"/> <output name="contrib_table" ftype="tabular"> <assert_contents> <has_text text="GeneCountPerGenome"/> <has_text text="OTUAbundanceInSample"/> </assert_contents> </output> </test> </tests> <help> <![CDATA[ @PICRUST_OVERVIEW@ **Command Documenation** This module outputs the relative contribution of OTUs to the predicted abundances of functions in your samples. The input biom file should be the output of normalize_by_copy_number. One output text file will be generated. Make sure that you specify an appropriate functional database for this command (usually the ko, cog, or rfam v13_5 database). ]]> </help> <expand macro="citations"/> </tool>