Mercurial > repos > bebatut > humann2

comparison humann2_rename_table.xml @ 0:3d6f37e7e3a8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty
author bebatut
date Thu, 26 May 2016 10:20:59 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:3d6f37e7e3a8
1 <tool id="humann2_rename_table" name="Rename" version="0.6.1">
2 <description>features of a HUMAnN2 generated table</description>
3
4 <macros>
5 <import>humann2_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9 <expand macro="stdio"/>
10
11 <version_command>
12 <![CDATA[
13 humann2_rename_table --version
14 ]]>
15 </version_command>
16
17 <command><![CDATA[
18 humann2_rename_table
19 -i $input_table
20 -o $output_table
21
22 --names $names
23 $simplify
24
25 -c $mapping_file
26 ]]></command>
27
28 <inputs>
29 <param name="input_table" type="data" format="tsv" label="Gene/pathway table" help="(-i)"/>
30
31 <param name="names" type="select" label="Table features that can be renamed" help="(--names)">
32 <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
33 <option value="metacyc-pwy">MetaCyc pathways</option>
34 <option value="ko">KEGG Orthogroups (KO)</option>
35 <option value="ec">Enzyme commision (EC)</option>
36 <option value="uniref50">UniRef50 gene families</option>
37 </param>
38
39 <param name='simplify' type='boolean' checked="false" truevalue='-s' falsevalue='' label="Remove non-alphanumeric characters from names?" help="(--simplify)"/>
40
41 <param name="mapping_file" type="data" format="tsv" label="Mapping file" help="The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new value (--custom)"/>
42
43 </inputs>
44
45 <outputs>
46 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" />
47 </outputs>
48
49 <tests>
50 <test>
51 <param name="input_table" value="expected_pathway_abundance.tsv"/>
52 <param name="names" value="metacyc-pwy" />
53 <param name='simplify' value=""/>
54 <param name="mapping_file" value="pathway_rename_mapping.tsv"/>
55 <output name="output_table" file="renamed_metacyc_pathways.tsv" />
56 </test>
57 </tests>
58
59 <help><![CDATA[
60 **What it does**
61
62 HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
63
64 Rename HUMAnN2 table features is a tool for renaming table features given a custom mapping. The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new valu
65 ]]></help>
66
67 <expand macro="citations"/>
68 </tool>