annotate topGO.xml @ 15:159596ec807d draft

planemo upload commit b8671ffe2e12dc6612b971a3e6e1dc71496aefd0-dirty
author proteore
date Fri, 24 Jan 2020 10:45:15 -0500
parents 35fc495473ec
children 7f1ce70f0f09
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
159596ec807d planemo upload commit b8671ffe2e12dc6612b971a3e6e1dc71496aefd0-dirty
proteore
parents: 14
diff changeset
1 <tool id="topGO" name="Enrichment analysis" version="2020.01.23">
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
2 <description>(Human, Mouse, Rat)[topGO]</description>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
3 <requirements>
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
4 <requirement type="package">R</requirement>
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
5 <requirement type="package">r-ggplot2</requirement>
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
6 <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement>
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
7 <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
8 <requirement type="package" version="3.8.2">bioconductor-org.rn.eg.db</requirement>
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
9 <!--requirement type="package" version="3.6.0">bioconductor-org.ce.eg.db</requirement-->
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
10 <!--requirement type="package" version="3.6.0">bioconductor-org.dm.eg.db</requirement-->
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
11 <!--requirement type="package" version="3.6.0">bioconductor-org.sc.sgd.db</requirement-->
9
70c0c8757f5f planemo upload commit 9d3e0b226140b566fc529fd0ffe7aa9e8388c6e5-dirty
proteore
parents: 8
diff changeset
12 <!--requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement-->
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
13 <requirement type="package" version="1.62.0">bioconductor-graph</requirement>
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
14 <requirement type="package" version="1.46.0">bioconductor-annotationdbi</requirement>
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
15 <requirement type="package" version="3.8.2">bioconductor-go.db</requirement>
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
16 <requirement type="package" version="2.36.0">bioconductor-topgo</requirement>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
17 </requirements>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
18 <stdio>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
19 <exit_code range="1:" />
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
20 </stdio>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
21 <command><![CDATA[
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
22
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
23 Rscript --vanilla $__tool_directory__/topGO_enrichment.R
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
24 --inputtype="$inputtype.filetype"
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
25 --input='$inputtype.genelist'
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
26
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
27 #if $inputtype.filetype == "file"
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
28 --column='$inputtype.column'
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
29 --header='$inputtype.header'
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
30 #end if
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
31
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
32 --ontology='$ontocat'
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
33 --option='$option'
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
34 --threshold='$threshold'
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
35 --correction='$correction'
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
36 --textoutput='true'
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
37 --plot='$plot'
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
38 --geneuniverse='$geneuniverse'
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
39 --background="$background_genes.background"
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
40
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
41 #if $background_genes.background == "true"
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
42 --background_genes="$background_genes.inputtype.genelist"
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
43 --background_input_type="$background_genes.inputtype.filetype"
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
44 #if $background_genes.inputtype.filetype == "file"
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
45 --background_header="$background_genes.inputtype.header"
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
46 --background_column="$background_genes.inputtype.column"
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
47 #end if
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
48 #end if
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
49
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
50 ]]></command>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
51
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
52 <inputs>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
53 <conditional name="inputtype">
12
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
54 <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene Id)" help="Copy/paste or from a file">
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
55 <option value="file" selected="true">Input file containing your IDs</option>
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
56 <option value="copy_paste">Copy/paste your list of IDs</option>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
57 </param>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
58 <when value="copy_paste">
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
59 <param name="genelist" type="text" label="Enter a list of IDs">
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
60 <sanitizer>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
61 <valid initial="string.printable">
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
62 <remove value="&apos;"/>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
63 </valid>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
64 <mapping initial="none">
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
65 <add source="&apos;" target="__sq__"/>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
66 </mapping>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
67 </sanitizer>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
68 </param>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
69 </when>
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
70 <when value="file">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
71 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
11
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
72 <param name="column" type="text" label="Column number of IDs" help="For example, fill in 'c1' if it is the first column, 'c2' if it is the second column and so on">
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
73 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
11
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
74 </param>
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
75 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
76 </when>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
77 </conditional>
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
78 <conditional name="background_genes">
12
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
79 <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Use your own background (ID list) ?"/>
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
80 <when value="true">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
81 <conditional name="inputtype">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
82 <param name="filetype" type="select" label="Enter your background IDs (Ensembl gene IDs)" help="(e.g : ENSG00000139618)">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
83 <option value="file" selected="true">Input file containing your background IDs</option>
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
84 <option value="copy_paste">Copy/paste your background IDs</option>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
85 </param>
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
86 <when value="copy_paste">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
87 <param name="genelist" type="text" label="Copy/paste your background IDs" help="IDs must be separated by spaces into the form field, for example: ENSG00000139618 ENSG00000007350">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
88 <sanitizer>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
89 <valid initial="string.printable">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
90 <remove value="&apos;"/>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
91 </valid>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
92 <mapping initial="none">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
93 <add source="&apos;" target="__sq__"/>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
94 </mapping>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
95 </sanitizer>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
96 </param>
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
97 </when>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
98 <when value="file">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
99 <param name="genelist" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help=""/>
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
100 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header ?" />
11
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
101 <param name="column" type="text" label="Column number of IDs" value="c1" help="For example, fill in 'c1' if it is the first column, 'c2' if it is the second column and so on">
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
102 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
103 </param>
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
104 </when>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
105 </conditional>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
106 </when>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
107 <when value="false"/>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
108 </conditional>
12
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
109 <param name="geneuniverse" type="select" label="Species (human, mouse, rat)">
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
110 <!--option value="org.At.tair.db" >Arabidopsis</option-->
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
111 <!--option value="org.Ce.eg.db" >Worm (C. elegans)</option-->
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
112 <!--option value="org.Dm.eg.db" >Fly (D. melanogaster)</option-->
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
113 <option value="org.Hs.eg.db" selected="true">Human (Homo sapiens)</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
114 <option value="org.Mm.eg.db" >Mouse (Mouse musculus)</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
115 <option value="org.Rn.eg.db" >Rat (Rattus norvegicus)</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
116 <!--option value="org.Sc.sgd.db" >Yeast (S. cerevisiae)</option-->
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
117 </param>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
118 <param name="ontocat" type="select" label="GO terms category">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
119 <option value="BP" >Biological Process</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
120 <option value="CC" >Cellular Component</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
121 <option value="MF" >Molecular Function</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
122 </param>
12
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
123 <param name="option" type="select" label="Select GO scoring method (read user doc section)">
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
124 <option value="classic" >Classic Fisher test</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
125 <option value="elim" selected="true">Elim</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
126 <option value="weight01" >Weight01</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
127 <option value="parentchild" >ParentChild</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
128 </param>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
129 <param name="threshold" type="text" label="p-value threshold (e.g : 1e-3)" value="1e-3"/>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
130 <param name="correction" label="Multiple testing procedure (p-value adjustment)" type="select">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
131 <option value="none" >None</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
132 <option value="holm">Holm correction</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
133 <option value="hochberg" >Hochberg correction</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
134 <option value="hommel" >Hommel correction</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
135 <option value="bonferroni" >Bonferroni correction</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
136 <option value="BH" selected="true">Benjamini and Hochberg</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
137 <option value="BY" >Benjamini and Yekutieli</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
138 <option value="fdr" >FDR</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
139 </param>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
140 <!--param name="textoutput" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a text file for results" /-->
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
141 <param name="plot" type="select" display="checkboxes" multiple="true" label="Graphical display" optional="false">
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
142 <option selected = "true" value="dotplot">dot-plot</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
143 <option value="barplot">bar-plot</option>
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
144 </param>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
145 </inputs>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
146 <outputs>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
147
11
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
148 <data name="outputtext" format="tsv" label="Text output for topGO analysis $ontocat category" from_work_dir="result.tsv">
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
149 <!--filter>textoutput</filter-->
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
150 </data>
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
151
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
152 <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png">
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
153 <filter>'dotplot' in plot</filter>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
154 </data>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
155
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
156 <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png">
11
fa2e27165d5d planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
proteore
parents: 10
diff changeset
157 <filter>'barplot' in plot</filter>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
158 </data>
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
159
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
160 </outputs>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
161 <tests>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
162 <test>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
163 <conditional name="inputtype">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
164 <param name="filetype " value="tabfile"/>
1
6788a57c5cb5 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
165 <param name="genelist" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/>
6788a57c5cb5 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
166 <param name="column" value="c8"/>
6788a57c5cb5 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
167 <param name="header" value="TRUE"/>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
168 </conditional>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
169 <param name="ontocat" value="BP"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
170 <param name="option" value="elim"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
171 <param name="threshold" value="1e-3"/>
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
172 <param name="correction" value="BH"/>
12
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
173 <param name="textoutput" value="TRUE"/>
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
174 <param name="plot" value="dotplot,barplot"/>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
175 <param name="geneuniverse" value="org.Hs.eg.db"/>
12
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
176 <output name="outputtext" file="result.tsv"/>
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
177 <output name="outputbarplot" file="barplot.png" compare="sim_size"/>
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
178 <output name="outputdotplot" file="dotplot.png" compare="sim_size"/>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
179 </test>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
180 </tests>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
181 <help><![CDATA[
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
182
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
183
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
184 **Description**
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
185
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
186 This tool is based on R package topGO. topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be applied.
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
187
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
188 This component computes 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 genes/proteins (of the selected species) associated associated with GO terms of the chosen category (BP,CC,MF).
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
189
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
190 -----
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
191
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
192 **Input required**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
193
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
194 This component works with Ensembl gene IDs (e.g : ENSG0000013618). You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab)
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
195 and then specifying the column number that contains the ENSG IDs.
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
196
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
197 -----
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
198
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
199 **Parameters**
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
200
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
201 "Species": "Species": the three available species are Homo sapiens, Mus musculus and Rattus norvegicus
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
202
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
203 "GO terms category": select either Biogical Process (BP)(by default), Cellular Component (CC) or Molecular Function (MF)
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
204
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
205 "Select GO scoring method: topGO provides the commonly used Fisher test for evaluating which GO terms are over-represented in your gene/protein list; it also provides other GO scoring algorithms (i.e. Elim, Weight01, Parentchild). For the merits of each option and their algorithmic description, please refer to topGO manual:
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
206 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
207
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
208 "p-value threshold (e.g : 1e-3)": must be in the form of "1e-5" (i.e. 0.00001)
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
209
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
210 "Multiple testing procedure (p-value adjustment): several FDR procedure for multiple testing and p-value adjustment are available: Holm, Hochberg
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
211 Hommel, Bonferroni, BH (Benjamini-Hochberg), BY (Benjamini-Yekutieli), FDR. Default is BH (most commonly used)
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
212
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
213 -----
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
214
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
215 **Output**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
216
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
217 Two types of output are available: textual and/or graphical outputs (barplot and/or a dotplot (set by default)).
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
218
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
219 *Textual output*
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
220
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
221 The text output lists all the GO-terms that were found significantly enriched according to the specified threshold (p-value).
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
222
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
223 The different fields are as follow:
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
224
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
225 - Annotated : number of genes in the selected species that are annotated with the GO-term.
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
226
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
227 - Significant : number of genes belonging to your input annotated with the GO-term.
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
228
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
229 - Expected : represents the expected number of interesting genes mapped to the GO term if the interesting genes were randomly distributed over all GO terms.
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
230
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
231 - p-values : p-value obtained after the test
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
232
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
233 - ( q-values : additional column with adjusted pvalues )
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
234
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
235 -----
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
236
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
237 .. class:: infomark
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
238
13
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
239 Packages used:
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
240 - bioconductor-org.hs.eg.db v3.8.2
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
241 - bioconductor-org.mm.eg.db v3.8.2
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
242 - bioconductor-org.rn.eg.db v3.8.2
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
243 - bioconductor-annotationdbi v1.46.0
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
244 - bioconductor-go.db v3.8.2
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
245 - bioconductor-graph v1.62.0
aba2aa04c7aa planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
proteore
parents: 12
diff changeset
246 - bioconductor-topgo v2.36.0
12
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
247
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
248 -----
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
249
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
250 .. class:: infomark
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
251
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
252 **Authors**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
253
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
254 Alexa A, Rahnenführer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006. 22(13):1600-7. PubMed PMID: 16606683.
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
255
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
256 -----
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
257
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
258 .. class:: infomark
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
259
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
260 **Galaxy integration**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
261
12
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
262 Lisa Perus, Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
263
10
e3430084c996 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents: 9
diff changeset
264 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
265
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
266 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
267
12
8eaa43ba1bfc planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 11
diff changeset
268 Help: contact@proteore.org for any questions or concerns about this tool.
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
269
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
270 ]]></help>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
271 <citations>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
272 </citations>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
273
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
274 </tool>