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comparison humann2_regroup_table.xml @ 0:1271ea9b43b6 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
author bebatut
date Mon, 20 Feb 2017 11:27:57 -0500
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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
4 <macros>
5 <import>humann2_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9 <expand macro="stdio"/>
10
11 <version_command>
12 <![CDATA[
13 humann2_regroup_table --version
14 ]]>
15 </version_command>
16
17 <command><![CDATA[
18 humann2_regroup_table
19 --input '$input'
20 -o '$output_table'
21 --function '$function'
22
23 #if $built_in.built_in_test == "true":
24 --groups '$built_in.gene_family_groups.groups'
25 #else:
26 --custom '$built_in.custom'
27 $built_in.reversed
28 #end if
29
30 --ungrouped '$ungrouped'
31 --protected '$protected'
32 ]]></command>
33
34 <inputs>
35 <param argument="--input" type="data" format="tsv" label="Gene/pathway table"/>
36 <param argument="--function" type="select" label="How to combine grouped features?">
37 <option value="sum" selected="true">Sum</option>
38 <option value="mean">Mean</option>
39 </param>
40 <conditional name="built_in">
41 <param name='built_in_test' type='select' label="Use built-in grouping options?" help="">
42 <option value="true" selected="true">Yes</option>
43 <option value="false">No</option>
44 </param>
45 <when value="true">
46 <conditional name="gene_family_groups">
47 <param name="gene_family_type" type="select" label="Gene family type">
48 <option value="uniref50">UniRef50 gene families</option>
49 <option value="uniref90">UniRef90 gene families</option>
50 </param>
51 <when value="uniref50">
52 <param name="groups" type="select" label="Grouping options" help="(--groups)">
53 <option value="uniref50_go">UniRef50 gene families into GO</option>
54 <option value="uniref50_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option>
55 <option value="uniref50_eggnog">UniRef50 gene families into eggNOG</option>
56 <option value="uniref50_pfam">UniRef50 gene families into PFAM</option>
57 <option value="uniref50_level4ec">UniRef50 gene families into level4ec</option>
58 <option value="uniref50_infogo1000">UniRef50 gene families into InfoGO1000</option>
59 <option value="uniref50_rxn">UniRef50 gene families into metacyc reactions</option>
60 </param>
61 </when>
62 <when value="uniref90">
63 <param name="groups" type="select" label="Grouping options" help="(--groups)">
64 <option value="uniref90_go">UniRef90 gene families into GO</option>
65 <option value="uniref90_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option>
66 <option value="uniref90_eggnog">UniRef90 gene families into eggNOG</option>
67 <option value="uniref90_pfam">UniRef90 gene families into PFAM</option>
68 <option value="uniref90_level4ec">UniRef90 gene families into level4ec</option>
69 <option value="uniref90_infogo1000">UniRef90 gene families into InfoGO1000</option>
70 <option value="uniref90_rxn">UniRef90 gene families into metacyc reactions</option>
71 </param>
72 </when>
73 </conditional>
74 </when>
75 <when value="false">
76 <param argument="--custom" type="data" format="tsv" label="Custom groups file"/>
77 <param argument='--reversed' type='boolean' checked="false" truevalue='--reversed' falsevalue='' label="Is the groups file reversed?" help="Mapping from features to groups"/>
78 </when>
79 </conditional>
80 <param argument="--precision" type="integer" value="3" label="Decimal places to round to after applying function"/>
81 <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?"/>
82 <param argument="--protected" type='boolean' checked="true" truevalue='Y' falsevalue='N' label="Carry through protected features, such as 'UNMAPPED'?"/>
83 </inputs>
84
85 <outputs>
86 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Regrouped table" />
87 </outputs>
88
89 <tests>
90 <test>
91 <param name="input" value="demo_genefamilies.tsv"/>
92 <param name="function" value="sum"/>
93 <param name="built_in_test" value="true"/>
94 <param name="gene_family_type" value="uniref90"/>
95 <param name="groups" value="uniref90_infogo1000"/>
96 <param name="ungrouped" value="Y"/>
97 <param name="protected" value="Y"/>
98 <output name="output_table" file="regrouped_gene_families_to_infogo1000.tsv"/>
99 </test>
100 <test>
101 <param name="input" value="demo_genefamilies.tsv"/>
102 <param name="function" value="mean"/>
103 <param name="built_in_test" value="true"/>
104 <param name="gene_family_type" value="uniref90"/>
105 <param name="groups" value="uniref90_ko"/>
106 <param name="ungrouped" value="Y"/>
107 <param name="protected" value="Y"/>
108 <output name="output_table" file="regrouped_gene_families_to_ko.tsv"/>
109 </test>
110 <test>
111 <param name="input" value="demo_genefamilies.tsv"/>
112 <param name="function" value="sum"/>
113 <param name="built_in_test" value="true"/>
114 <param name="gene_family_type" value="uniref90"/>
115 <param name="groups" value="uniref90_rxn"/>
116 <param name="ungrouped" value="Y"/>
117 <param name="protected" value="Y"/>
118 <output name="output_table" file="regrouped_gene_families_to_rxn.tsv"/>
119 </test>
120 </tests>
121
122 <help><![CDATA[
123 **What it does**
124
125 HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
126
127 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.
128 ]]></help>
129
130 <expand macro="citations"/>
131 </tool>