Mercurial > repos > iuc > humann2_rename_table

comparison humann2_rename_table.xml @ 0:dd4b5b9daf6b draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
author iuc
date Mon, 13 Mar 2017 12:37:08 -0400
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-1:000000000000 0:dd4b5b9daf6b
1 <tool id="humann2_rename_table" name="Rename" version="@WRAPPER_VERSION@.0">
2 <description>features of a HUMAnN2 generated table</description>
3 <macros>
4 <import>humann2_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version"/>
8 <command detect_errors="exit_code"><![CDATA[
9 humann2_rename_table
10 --input '$input'
11 -o '$output_table'
12 --names '$names'
13 $simplify
14 #if $custom
15 --custom '$custom'
16 #end if
17 ]]></command>
18 <inputs>
19 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
20 <param argument="--names" type="select" label="Table features that can be renamed">
21 <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
22 <option value="metacyc-pwy">MetaCyc pathways</option>
23 <option value="infogo1000">InfoGO1000</option>
24 <option value="uniref90">UniRef90</option>
25 <option value="kegg-module">KEGG Module</option>
26 <option value="ec">Enzyme commision (EC)</option>
27 <option value="go">Gene Ontology (GO)</option>
28 <option value="pfam">PFAM</option>
29 <option value="eggnog">eggNOG</option>
30 <option value="uniref50">UniRef50</option>
31 <option value="kegg-pathway">KEGG Pathway</option>
32 <option value="kegg-orthology">KEGG Orthology</option>
33 </param>
34 <param argument="--simplify" type="boolean" checked="false" truevalue="--simplify" falsevalue="" label="Remove non-alphanumeric characters from names?"/>
35 <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"/>
36 </inputs>
37 <outputs>
38 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" />
39 </outputs>
40 <tests>
41 <test>
42 <param name="input" value="demo_genefamilies.tsv"/>
43 <param name="names" value="uniref90" />
44 <param name="simplify" value=""/>
45 <output name="output_table">
46 <assert_contents>
47 <has_text text="UniRef90_R6I0Z3: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" />
48 <has_text text="UniRef90_I9RGY5: Tape measure domain-containing protein|g__Bacteroides.s__Bacteroides_dorei" />
49 <has_text text="UniRef90_C3RF26: HRDC domain protein" />
50 </assert_contents>
51 </output>
52 </test>
53 </tests>
54 <help><![CDATA[
55 @HELP_HEADER@
56
57 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
58 ]]></help>
59 <expand macro="citations"/>
60 </tool>