Mercurial > repos > iuc > humann2_rename_table
comparison humann2_rename_table.xml @ 1:b6d4c448782f draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author | iuc |
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date | Tue, 01 Aug 2017 07:55:21 -0400 |
parents | dd4b5b9daf6b |
children | 252ae00df89c |
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0:dd4b5b9daf6b | 1:b6d4c448782f |
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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[ |