Mercurial > repos > iuc > picrust_metagenome_contributions

annotate metagenome_contributions.xml @ 5:857e8724b43f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 899e24f2aecad79c80667fb6c938dd4573a98820
author iuc
date Fri, 09 Feb 2024 21:42:03 +0000
parents f0f5028a3393
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
f0f5028a3393 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents: 0
diff changeset
1 <tool id="picrust_metagenome_contributions" name="Metagenome Contributions" version="@TOOL_VERSION@.0">
0
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
2 <description>of OTUs to user-specified functions</description>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
3 <macros>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
4 <import>macros.xml</import>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
5 </macros>
5
857e8724b43f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 899e24f2aecad79c80667fb6c938dd4573a98820
iuc
parents: 4
diff changeset
6 <expand macro="bio_tools"/>
0
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
8 <expand macro="version_command"/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
10 metagenome_contributions.py
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
11 -i '$input_data'
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
12 -o '$contrib_table'
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
13 -c '$gg.precalc'
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
14 -l '$limit_gene'
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
15 ]]></command>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
16 <inputs>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
17 <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."/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
18 <expand macro="otu-reference-precalculated"/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
19 <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." />
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
20 </inputs>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
21 <outputs>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
22 <data name="contrib_table" format="tabular"/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
23 </outputs>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
24 <tests>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
25 <test>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
26 <param name="input_data" value="otu_table_for_custom_trait_table.biom"/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
27 <param name="source" value="hist"/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
28 <param name="precalc" value="custom_trait_table.tab"/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
29 <output name="contrib_table" ftype="tabular">
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
30 <assert_contents>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
31 <has_text text="GeneCountPerGenome"/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
32 <has_text text="OTUAbundanceInSample"/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
33 </assert_contents>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
34 </output>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
35 </test>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
36 </tests>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
37 <help>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
38 <![CDATA[
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
39 @PICRUST_OVERVIEW@
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
40
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
41 **Command Documenation**
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
42
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
43 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.
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
44
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
45 Make sure that you specify an appropriate functional database for this command (usually the ko, cog, or rfam v13_5 database).
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
46
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
47 ]]>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
48 </help>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
49 <expand macro="citations"/>
b0a55e81a3dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
diff changeset
50 </tool>