Mercurial > repos > iuc > humann2_rename_table

comparison humann2_rename_table.xml @ 1:b6d4c448782f draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author iuc
date Tue, 01 Aug 2017 07:55:21 -0400
parents dd4b5b9daf6b
children 252ae00df89c
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0:dd4b5b9daf6b 1:b6d4c448782f
4 <import>humann2_macros.xml</import> 4 <import>humann2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version"/> 7 <expand macro="version"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 humann2_rename_table 9 humann2_rename_table
10 --input '$input' 10 --input '$input'
11 -o '$output_table' 11 -o '$output_table'
12 --names '$names' 12 #if $renaming.type == 'standard'
13 $simplify 13 --names '$renaming.names'
14 #if $custom 14 #else
15 --custom '$custom' 15 --custom '$renaming.custom'
16 #end if 16 #end if
17 $simplify
17 ]]></command> 18 ]]></command>
18 <inputs> 19 <inputs>
19 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/> 20 <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 <conditional name="renaming">
21 <option value="metacyc-rxn" selected="true">MetaCyc reactions</option> 22 <param name="type" type="select" label="Type of renaming">
22 <option value="metacyc-pwy">MetaCyc pathways</option> 23 <option value="standard">Standard renaming</option>
23 <option value="infogo1000">InfoGO1000</option> 24 <option value="custom">Custom renaming</option>
24 <option value="uniref90">UniRef90</option> 25 </param>
25 <option value="kegg-module">KEGG Module</option> 26 <when value="standard">
26 <option value="ec">Enzyme commision (EC)</option> 27 <param argument="--names" type="select" label="Table features that can be renamed">
27 <option value="go">Gene Ontology (GO)</option> 28 <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
28 <option value="pfam">PFAM</option> 29 <option value="metacyc-pwy">MetaCyc pathways</option>
29 <option value="eggnog">eggNOG</option> 30 <option value="infogo1000">InfoGO1000</option>
30 <option value="uniref50">UniRef50</option> 31 <option value="kegg-module">KEGG Module</option>
31 <option value="kegg-pathway">KEGG Pathway</option> 32 <option value="ec">Enzyme commision (EC)</option>
32 <option value="kegg-orthology">KEGG Orthology</option> 33 <option value="go">Gene Ontology (GO)</option>
33 </param> 34 <option value="pfam">PFAM</option>
34 <param argument="--simplify" type="boolean" checked="false" truevalue="--simplify" falsevalue="" label="Remove non-alphanumeric characters from names?"/> 35 <option value="eggnog">eggNOG</option>
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 <option value="uniref50">UniRef50</option>
37 <!--<option value="uniref90">UniRef90</option>-->
38 <option value="kegg-pathway">KEGG Pathway</option>
39 <option value="kegg-orthology">KEGG Orthology</option>
40 </param>
41 </when>
42 <when value="custom">
43 <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"/>
44 </when>
45 </conditional>
46 <param argument="--simplify" type="boolean" truevalue="--simplify" falsevalue="" checked="false" label="Remove non-alphanumeric characters from names?"/>
36 </inputs> 47 </inputs>
37 <outputs> 48 <outputs>
38 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" /> 49 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" />
39 </outputs> 50 </outputs>
40 <tests> 51 <tests>
41 <test> 52 <test>
42 <param name="input" value="demo_genefamilies.tsv"/> 53 <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/>
43 <param name="names" value="uniref90" /> 54 <conditional name="renaming">
55 <param name="type" value="standard"/>
56 <param name="names" value="infogo1000" />
57 </conditional>
44 <param name="simplify" value=""/> 58 <param name="simplify" value=""/>
45 <output name="output_table"> 59 <output name="output_table">
46 <assert_contents> 60 <assert_contents>
47 <has_text text="UniRef90_R6I0Z3: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" /> 61 <has_text text="GO:0000015: [CC] phosphopyruvate hydratase complex" />
48 <has_text text="UniRef90_I9RGY5: Tape measure domain-containing protein|g__Bacteroides.s__Bacteroides_dorei" /> 62 <has_text text="GO:0000287: [MF] magnesium ion binding" />
49 <has_text text="UniRef90_C3RF26: HRDC domain protein" /> 63 </assert_contents>
64 </output>
65 </test>
66 <test>
67 <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/>
68 <conditional name="renaming">
69 <param name="type" value="custom"/>
70 <param name="custom" value="rename_mapping" />
71 </conditional>
72 <param name="simplify" value=""/>
73 <output name="output_table">
74 <assert_contents>
75 <has_text text="GO:0000015: GO1" />
76 <has_text text="GO:0000107: NO_NAME" />
50 </assert_contents> 77 </assert_contents>
51 </output> 78 </output>
52 </test> 79 </test>
53 </tests> 80 </tests>
54 <help><![CDATA[ 81 <help><![CDATA[