Mercurial > repos > proteore > proteore_topgo

annotate topGO.xml @ 0:92dfcfb03add draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
author proteore
date Wed, 22 Aug 2018 10:39:30 -0400
parents
children 5569a3f066cf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
1 <tool id="topGO" name="topGO" version="2018.08.22">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
2 <description>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
3 Enrichment analysis for Gene Ontology
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
4 </description>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
5 <requirements>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
6 <requirement type="package" version="3.4.1">R</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
7 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
8 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
9 <requirement type="package" version="1.56.0">bioconductor-graph</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
10 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
11 <requirement type="package" version="3.5.0">bioconductor-go.db</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
12 <requirement type="package" version="2.30.0">bioconductor-topgo</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
13 </requirements>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
14 <stdio>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
15 <exit_code range="1:" />
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
16 </stdio>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
17 <command><![CDATA[
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
18
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
19 #if $inputtype.filetype == "file_all":
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
20 Rscript --vanilla $__tool_directory__/enrichment_v3.R
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
21 --inputtype tabfile
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
22 --input '$inputtype.genelist'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
23 --ontology '$ontocat'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
24 --option '$option'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
25 --threshold '$threshold'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
26 --correction '$correction'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
27 --textoutput '$condtext.textoutput'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
28 --barplotoutput '$condbar.barplotoutput'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
29 --dotplotoutput '$conddot.dotplotoutput'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
30 --column '$inputtype.column'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
31 --geneuniverse '$geneuniverse'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
32 --header '$inputtype.header'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
33 #end if
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
34
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
35
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
36 #if $inputtype.filetype == "copy_paste":
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
37 Rscript --vanilla $__tool_directory__/enrichment_v3.R
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
38 --inputtype copypaste
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
39 --input '$inputtype.genelist'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
40 --ontology '$ontocat'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
41 --option '$option'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
42 --threshold '$threshold'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
43 --correction '$correction'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
44 --textoutput '$condtext.textoutput'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
45 --barplotoutput '$condbar.barplotoutput'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
46 --dotplotoutput '$conddot.dotplotoutput'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
47 --column c1
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
48 --geneuniverse '$geneuniverse'
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
49 --header None
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
50 #end if
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
51
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
52
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
53
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
54 ]]></command>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
55
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
56 <inputs>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
57 <conditional name="inputtype">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
58 <param name="filetype" type="select" label="Select your type of input file" help="The identifiers must be Ensembl gene IDs (e.g : ENSG00000139618). If it is not the case, please use the ID Mapping tool.">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
59 <option value="file_all" selected="true">Input file containing your identifiers</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
60 <option value="copy_paste">Copy/paste your list of IDs</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
61 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
62 <when value="copy_paste">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
63 <param name="genelist" type="text" label="Enter a list of identifiers">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
64 <sanitizer>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
65 <valid initial="string.printable">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
66 <remove value="&apos;"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
67 </valid>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
68 <mapping initial="none">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
69 <add source="&apos;" target="__sq__"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
70 </mapping>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
71 </sanitizer>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
72 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
73 </when>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
74 <when value="file_all">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
75 <param name="genelist" type="data" format="txt,tabular" label="Choose an input file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
76 <param name="column" type="text" label="Please specify the column where you would like to apply the comparison (e.g : Enter c1)" value="c1"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
77
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
78 <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
79 <option value="TRUE" selected="true">Yes</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
80 <option value="FALSE" selected="false">No</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
81 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
82 </when>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
83 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
84 <param name="geneuniverse" type="select" label="Select a specie">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
85 <option value="org.At.tair.db" >Arabidopsis</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
86 <option value="org.Ce.eg.db" >C.elegans</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
87 <option value="org.Dm.eg.db" >Fly</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
88 <option value="org.Hs.eg.db" selected="true">Human</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
89 <option value="org.Mm.eg.db" >Mouse</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
90 <option value="org.Sc.sqd.db" >Yeast</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
91 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
92
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
93 <param name="ontocat" type="select" label="Ontology category">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
94 <option value="BP" >Biological Process</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
95 <option value="CC" >Cellular Component</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
96 <option value="MF" >Molecular Function</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
97 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
98
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
99 <param name="option" type="select" label="Choose the topGO option for your analysis">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
100 <option value="classic" >Classic fisher test</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
101 <option value="elim" selected="true">Elim</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
102 <option value="weight01" >Weight01</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
103 <option value="parentchild" >ParentChild</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
104 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
105 <param name="threshold" type="text" label="Enter the p-value threshold level under the form 1e-level wanted (e.g : 1e-3)" value="1e-3"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
106 <param name="correction" label="Choose a correction for multiple testing" type="select">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
107 <option value="none" >None</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
108 <option value="holm">Holm correction</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
109 <option value="hochberg" >Hochberg correction</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
110 <option value="hommel" >Hommel correction</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
111 <option value="bonferroni" >Bonferroni correction</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
112 <option value="BH" selected="true">Benjamini and Hochberg</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
113 <option value="BY" >Benjamini and Yekutieli</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
114 <option value="fdr" >FDR</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
115 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
116 <conditional name="condtext">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
117 <param name="textoutput" type="select" label="Generate a text file for results">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
118 <option value="TRUE">Yes</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
119 <option value="FALSE">No</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
120 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
121 <when value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
122 <when value="FALSE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
123 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
124 <conditional name="condbar">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
125 <param name="barplotoutput" type="select" label="Generate a barplot of over-represented GO terms">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
126 <option value="TRUE">Yes</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
127 <option value="FALSE">No</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
128 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
129 <when value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
130 <when value="FALSE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
131 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
132 <conditional name="conddot">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
133 <param name="dotplotoutput" type="select" label="Generate a dotplot of over-represented GO terms">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
134 <option value="TRUE">Yes</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
135 <option value="FALSE">No</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
136 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
137 <when value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
138 <when value="FALSE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
139 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
140 </inputs>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
141 <outputs>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
142
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
143 <data name="outputtext" format="tabular" label="Text output for topGO analysis $ontocat category" from_work_dir="result.csv">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
144 <filter>condtext['textoutput']=="TRUE"</filter>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
145 </data>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
146
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
147 <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
148 <filter>condbar['barplotoutput']=="TRUE"</filter>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
149 </data>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
150
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
151 <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
152 <filter>conddot['dotplotoutput']=="TRUE"</filter>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
153 </data>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
154
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
155 </outputs>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
156 <tests>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
157 <test>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
158 <conditional name="inputtype">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
159 <param name="filetype " value="tabfile"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
160 <param name="genelist" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
161 <param name="column" value="c8"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
162 <param name="header" value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
163 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
164 <param name="ontocat" value="BP"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
165 <param name="option" value="elim"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
166 <param name="threshold" value="1e-3"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
167 <param name="correction" value="BH"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
168 <conditional name="condtext">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
169 <param name="textoutput" value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
170 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
171 <conditional name="condbar">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
172 <param name="barplotoutput" value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
173 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
174 <conditional name="conddot">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
175 <param name="dotoutput" value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
176 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
177 <param name="geneuniverse" value="org.Hs.eg.db"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
178 <output name="outputtext" file="Text_output_for_topGO_analysis_BP_category.tabular"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
179 <output name="outputbarplot" file="Barplot_output_for_topGO_analysis_BP_category.png"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
180 <output name="outputdotplot" file="Dotplot_output_for_topGO_analysis_BP_category.png"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
181 </test>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
182 </tests>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
183 <help><![CDATA[
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
184
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
185
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
186 **Galaxy component based on R package topGO.**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
187
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
188 **Input required**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
189
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
190 This component works with Ensembl gene ids (e.g : ENSG0000013618). You can
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
191 copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab)
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
192 where there are contained.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
193
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
194 **Principle**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
195
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
196 This component provides the GO terms representativity of a gene list in one ontology category (Biological Process "BP", Cellular Component "CC", Molecular Function "MF"). This representativity is evaluated in comparison to the background list of all human genes associated associated with GO terms of the chosen category (BP,CC,MF). This background is given by the R package "org.Hs.eg.db", which is a genome wide association package for **human**.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
197
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
198 **Output**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
199
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
200 Three kind of outputs are available : a textual output, a barplot output and
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
201 a dotplot output.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
202
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
203 *Textual output* :
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
204 The text output lists all the GO-terms that were found significant under the specified threshold.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
205
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
206
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
207 The different fields are as follow :
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
208
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
209 - Annotated : number of genes in org.Hs.eg.db which are annotated with the GO-term.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
210
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
211 - Significant : number of genes belonging to your input which are annotated with the GO-term.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
212
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
213 - Expected : show an estimate of the number of genes a node of size Annotated would have if the significant genes were to be randomly selected from the gene universe.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
214
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
215 - pvalues : pvalue obtained after the test
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
216
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
217 - ( qvalues : additional column with adjusted pvalues )
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
218
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
219
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
220 **Tests**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
221
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
222 topGO provides a classic fisher test for evaluating if some GO terms are over-represented in your gene list, but other options are also provided (elim, weight01,parentchild). For the merits of each option and their algorithmic descriptions, please refer to topGO manual :
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
223 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
224
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
225 **Multiple testing corrections**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
226
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
227 Furthermore, the following corrections for multiple testing can also be applied :
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
228
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
229 - holm
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
230
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
231 - hochberg
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
232
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
233 - hommel
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
234
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
235 - bonferroni
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
236
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
237 - BH
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
238
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
239 - BY
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
240
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
241 - fdr
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
242
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
243 -----
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
244
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
245 .. class:: infomark
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
246
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
247 **Authors**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
248
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
249 Alexa A and Rahnenfuhrer J (2016). topGO: Enrichment Analysis for Gene Ontology. R package version 2.30.0.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
250
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
251 **Galaxy integration**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
252
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
253 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
254
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
255 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
256
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
257 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
258
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
259 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
260
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
261 ]]></help>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
262 <citations>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
263 </citations>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
264
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
265 </tool>