Mercurial > repos > iuc > picrust_metagenome_contributions
diff metagenome_contributions.xml @ 0:b0a55e81a3dd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
author | iuc |
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date | Wed, 30 Aug 2017 04:49:13 -0400 |
parents | |
children | f0f5028a3393 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metagenome_contributions.xml Wed Aug 30 04:49:13 2017 -0400 @@ -0,0 +1,49 @@ +<tool id="picrust_metagenome_contributions" name="Metagenome Contributions" version="@WRAPPER_VERSION@.0"> + <description>of OTUs to user-specified functions</description> + <macros> + <import>macros.xml</import> + </macros> + <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>