Mercurial > repos > iuc > humann2_regroup_table
comparison humann2_regroup_table.xml @ 0:a1747df2bc21 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
author | iuc |
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date | Mon, 13 Mar 2017 12:38:02 -0400 |
parents | |
children | 1d141730ec69 |
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-1:000000000000 | 0:a1747df2bc21 |
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1 <tool id="humann2_regroup_table" name="Regroup" version="@WRAPPER_VERSION@.0"> | |
2 <description> a HUMAnN2 generated table by features</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_regroup_table | |
10 --input '$input' | |
11 -o '$output_table' | |
12 --function '$function' | |
13 | |
14 #if $built_in.built_in_test == "true": | |
15 --groups '$built_in.gene_family_groups.groups' | |
16 #else: | |
17 --custom '$built_in.custom' | |
18 $built_in.reversed | |
19 #end if | |
20 | |
21 --ungrouped '$ungrouped' | |
22 --protected '$protected' | |
23 ]]></command> | |
24 <inputs> | |
25 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/> | |
26 <param argument="--function" type="select" label="How to combine grouped features?"> | |
27 <option value="sum" selected="true">Sum</option> | |
28 <option value="mean">Mean</option> | |
29 </param> | |
30 <conditional name="built_in"> | |
31 <param name="built_in_test" type="select" label="Use built-in grouping options?" help=""> | |
32 <option value="true" selected="true">Yes</option> | |
33 <option value="false">No</option> | |
34 </param> | |
35 <when value="true"> | |
36 <conditional name="gene_family_groups"> | |
37 <param name="gene_family_type" type="select" label="Gene family type"> | |
38 <option value="uniref50">UniRef50 gene families</option> | |
39 <option value="uniref90">UniRef90 gene families</option> | |
40 </param> | |
41 <when value="uniref50"> | |
42 <param name="groups" type="select" label="Grouping options" help="(--groups)"> | |
43 <option value="uniref50_go">UniRef50 gene families into GO</option> | |
44 <option value="uniref50_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option> | |
45 <option value="uniref50_eggnog">UniRef50 gene families into eggNOG</option> | |
46 <option value="uniref50_pfam">UniRef50 gene families into PFAM</option> | |
47 <option value="uniref50_level4ec">UniRef50 gene families into level4ec</option> | |
48 <option value="uniref50_infogo1000">UniRef50 gene families into InfoGO1000</option> | |
49 <option value="uniref50_rxn">UniRef50 gene families into metacyc reactions</option> | |
50 </param> | |
51 </when> | |
52 <when value="uniref90"> | |
53 <param name="groups" type="select" label="Grouping options" help="(--groups)"> | |
54 <option value="uniref90_go">UniRef90 gene families into GO</option> | |
55 <option value="uniref90_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option> | |
56 <option value="uniref90_eggnog">UniRef90 gene families into eggNOG</option> | |
57 <option value="uniref90_pfam">UniRef90 gene families into PFAM</option> | |
58 <option value="uniref90_level4ec">UniRef90 gene families into level4ec</option> | |
59 <option value="uniref90_infogo1000">UniRef90 gene families into InfoGO1000</option> | |
60 <option value="uniref90_rxn">UniRef90 gene families into metacyc reactions</option> | |
61 </param> | |
62 </when> | |
63 </conditional> | |
64 </when> | |
65 <when value="false"> | |
66 <param argument="--custom" type="data" format="tsv" label="Custom groups file"/> | |
67 <param argument="--reversed" type="boolean" checked="false" truevalue="--reversed" falsevalue="" label="Is the groups file reversed?" help="Mapping from features to groups"/> | |
68 </when> | |
69 </conditional> | |
70 <param argument="--precision" type="integer" value="3" label="Decimal places to round to after applying function"/> | |
71 <param argument="--ungrouped" type="boolean" checked="true" truevalue="Y" falsevalue="N" label="Include an 'UNGROUPED' group to capture features that did not belong to other groups?"/> | |
72 <param argument="--protected" type="boolean" checked="true" truevalue="Y" falsevalue="N" label="Carry through protected features, such as 'UNMAPPED'?"/> | |
73 </inputs> | |
74 <outputs> | |
75 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Regrouped table" /> | |
76 </outputs> | |
77 <tests> | |
78 <test> | |
79 <param name="input" value="demo_genefamilies.tsv"/> | |
80 <param name="function" value="sum"/> | |
81 <param name="built_in_test" value="true"/> | |
82 <param name="gene_family_type" value="uniref90"/> | |
83 <param name="groups" value="uniref90_infogo1000"/> | |
84 <param name="ungrouped" value="Y"/> | |
85 <param name="protected" value="Y"/> | |
86 <output name="output_table" file="regrouped_gene_families_to_infogo1000.tsv"/> | |
87 </test> | |
88 <test> | |
89 <param name="input" value="demo_genefamilies.tsv"/> | |
90 <param name="function" value="mean"/> | |
91 <param name="built_in_test" value="true"/> | |
92 <param name="gene_family_type" value="uniref90"/> | |
93 <param name="groups" value="uniref90_ko"/> | |
94 <param name="ungrouped" value="Y"/> | |
95 <param name="protected" value="Y"/> | |
96 <output name="output_table" file="regrouped_gene_families_to_ko.tsv"/> | |
97 </test> | |
98 <test> | |
99 <param name="input" value="demo_genefamilies.tsv"/> | |
100 <param name="function" value="sum"/> | |
101 <param name="built_in_test" value="true"/> | |
102 <param name="gene_family_type" value="uniref90"/> | |
103 <param name="groups" value="uniref90_rxn"/> | |
104 <param name="ungrouped" value="Y"/> | |
105 <param name="protected" value="Y"/> | |
106 <output name="output_table" file="regrouped_gene_families_to_rxn.tsv"/> | |
107 </test> | |
108 </tests> | |
109 <help><![CDATA[ | |
110 @HELP_HEADER@ | |
111 | |
112 Regroup HUMAnN2 table features is a tool for regrouping table features (abundances or coverage) given a table of feature values and a mapping of groups to component features. It produces a new table with group values in place of feature values. | |
113 ]]></help> | |
114 <expand macro="citations"/> | |
115 </tool> |