Mercurial > repos > iuc > qiime_filter_taxa_from_otu_table
view filter_taxa_from_otu_table.xml @ 5:95a39cd8a53a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
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date | Sat, 05 Aug 2017 07:32:36 -0400 |
parents | 9209e7b16b05 |
children | 13ad599d3fe3 |
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<tool id="qiime_filter_taxa_from_otu_table" name="Filter taxa from an OTU table" version="@WRAPPER_VERSION@.0"> <description>(filter_taxa_from_otu_table)</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>filter_taxa_from_otu_table.py --version</version_command> <command detect_errors="aggressive"><![CDATA[ filter_taxa_from_otu_table.py --input_otu_table_fp '$input_otu_table_fp' --output_otu_table_fp '$output_otu_table_fp' #if str($positive_taxa) != '' --positive_taxa '$positive_taxa' #end if #if str($negative_taxa) != '' --negative_taxa '$negative_taxa' #end if --metadata_field '$metadata_field' ]]></command> <inputs> <param argument="--input_otu_table_fp" type="data" format="biom1" label="Input OTU table to filter"/> <param argument="--positive_taxa" type="text" label="Comma-separated list of taxa to retain" optional="True"/> <param argument="--negative_taxa" type="text" label="Comma-separated list of taxa to discard" optional="True"/> <param argument="--metadata_field" type="text" value="taxonomy" label="Observation metadata identifier to filter based on"/> </inputs> <outputs> <data name="output_otu_table_fp" format="biom1" label="${tool.name} on ${on_string}: Filtered OTU table"/> </outputs> <tests> <test> <param name="input_otu_table_fp" value="filter_taxa_from_otu_table/otu_table.biom"/> <param name="positive_taxa" value="p__Bacteroidetes,p__Firmicutes"/> <param name="metadata_field" value="taxonomy"/> <output name="output_otu_table_fp" file="filter_taxa_from_otu_table/positive_taxa.biom" ftype="biom1" compare="sim_size" delta="20"/> </test> <test> <param name="input_otu_table_fp" value="filter_taxa_from_otu_table/otu_table.biom"/> <param name="negative_taxa" value="p__Bacteroidetes,p__Firmicutes"/> <param name="metadata_field" value="taxonomy"/> <output name="output_otu_table_fp" file="filter_taxa_from_otu_table/negative_taxa.biom" ftype="biom1" compare="sim_size" delta="20"/> </test> <test> <param name="input_otu_table_fp" value="filter_taxa_from_otu_table/otu_table.biom"/> <param name="positive_taxa" value="p__Firmicutes"/> <param name="negative_taxa" value="c__Clostridia"/> <param name="metadata_field" value="taxonomy"/> <output name="output_otu_table_fp" file="filter_taxa_from_otu_table/positive_negative_taxa.biom" ftype="biom1" compare="sim_size" delta="20"/> </test> </tests> <help><![CDATA[ **What it does** This scripts filters an OTU table based on taxonomic metadata. It can be applied for positive filtering (i.e., keeping only certain taxa), negative filtering (i.e., discarding only certain taxa), or both at the same time. ]]></help> <citations> <expand macro="citations"/> </citations> </tool>