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comparison humann2_rename_table.xml @ 0:993b75cba608 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
author bebatut
date Mon, 20 Feb 2017 11:29:37 -0500
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1 <tool id="humann2_rename_table" name="Rename" version="@WRAPPER_VERSION@.0">
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 --input '$input'
20 -o '$output_table'
21 --names '$names'
22 $simplify
23 #if $custom
24 --custom '$custom'
25 #end if
26 ]]></command>
27
28 <inputs>
29 <param argument="--input" type="data" format="tsv" label="Gene/pathway table"/>
30
31 <param argument="--names" type="select" label="Table features that can be renamed">
32 <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
33 <option value="metacyc-pwy">MetaCyc pathways</option>
34 <option value="infogo1000">InfoGO1000</option>
35 <option value="uniref90">UniRef90</option>
36 <option value="kegg-module">KEGG Module</option>
37 <option value="ec">Enzyme commision (EC)</option>
38 <option value="go">Gene Ontology (GO)</option>
39 <option value="pfam">PFAM</option>
40 <option value="eggnog">eggNOG</option>
41 <option value="uniref50">UniRef50</option>
42 <option value="kegg-pathway">KEGG Pathway</option>
43 <option value="kegg-orthology">KEGG Orthology</option>
44 </param>
45 <param argument='--simplify' type='boolean' checked="false" truevalue='--simplify' falsevalue='' label="Remove non-alphanumeric characters from names?"/>
46 <param argument="--custom" 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" optional="true"/>
47 </inputs>
48
49 <outputs>
50 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" />
51 </outputs>
52
53 <tests>
54 <test>
55 <param name="input" value="demo_genefamilies.tsv"/>
56 <param name="names" value="uniref90" />
57 <param name='simplify' value=""/>
58 <output name="output_table">
59 <assert_contents>
60 <has_text text="UniRef90_R6I0Z3: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" />
61 <has_text text="UniRef90_I9RGY5: Tape measure domain-containing protein|g__Bacteroides.s__Bacteroides_dorei" />
62 <has_text text="UniRef90_C3RF26: HRDC domain protein" />
63 </assert_contents>
64 </output>
65 </test>
66 </tests>
67
68 <help><![CDATA[
69 **What it does**
70
71 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>`_.
72
73 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
74 ]]></help>
75
76 <expand macro="citations"/>
77 </tool>