Mercurial > repos > iuc > picrust_metagenome_contributions

diff metagenome_contributions.xml @ 0:b0a55e81a3dd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
author iuc
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
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+<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>