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
date Mon, 13 Mar 2017 12:38:02 -0400
parents
children 1d141730ec69
comparison
equal deleted inserted replaced
-1:000000000000 0:a1747df2bc21
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>