Mercurial > repos > proteore > proteore_topgo

annotate topGO.xml @ 8:ddaa0c318d65 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
author proteore
date Fri, 23 Mar 2018 10:43:32 -0400
parents 1b2b81169c66
children 70c0c8757f5f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
ce67a81ef27e planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty
proteore
parents: 5
diff changeset
1 <tool id="topGO" name="topGO" version="0.1.0">
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
2 <description>
7
1b2b81169c66 planemo upload commit 4f0554e513548e208e1b0c5efc349b9daa6a6349-dirty
proteore
parents: 6
diff changeset
3 Enrichment analysis for Gene Ontology
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
4 </description>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
5 <requirements>
2
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
6 <requirement type="package" version="3.4.1">R</requirement>
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
7 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
4
288d10aa2497 planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents: 3
diff changeset
8 <requirement type="package" version="3.4.1">bioconductor-org.hs.eg.db</requirement>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
9 <requirement type="package" version="1.54.0">bioconductor-graph</requirement>
5
829cbdb71efa planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents: 4
diff changeset
10 <requirement type="package" version="1.38.2">bioconductor-annotationdbi</requirement>
829cbdb71efa planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents: 4
diff changeset
11 <requirement type="package" version="3.4.1">bioconductor-go.db</requirement>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
12 <requirement type="package" version="2.28.0">bioconductor-topgo</requirement>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
13 </requirements>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
14 <stdio>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
15 <exit_code range="1:" />
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
16 </stdio>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
17 <command><![CDATA[
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
18
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
19 #if $inputtype.filetype == "file_all":
2
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
20 Rscript --vanilla $__tool_directory__/enrichment_v3.R
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
21 --inputtype tabfile
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
22 --input '$inputtype.genelist'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
23 --ontology '$ontocat'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
24 --option '$option'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
25 --threshold '$threshold'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
26 --correction '$correction'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
27 --textoutput '$condtext.textoutput'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
28 --barplotoutput '$condbar.barplotoutput'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
29 --dotplotoutput '$conddot.dotplotoutput'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
30 --column '$inputtype.column'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
31 --geneuniverse '$geneuniverse'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
32 --header '$inputtype.header'
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
33 #end if
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
34
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
35
2
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
36 #if $inputtype.filetype == "copy_paste":
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
37 Rscript --vanilla $__tool_directory__/enrichment_v3.R
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
38 --inputtype copypaste
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
39 --input '$inputtype.genelist'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
40 --ontology '$ontocat'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
41 --option '$option'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
42 --threshold '$threshold'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
43 --correction '$correction'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
44 --textoutput '$condtext.textoutput'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
45 --barplotoutput '$condbar.barplotoutput'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
46 --dotplotoutput '$conddot.dotplotoutput'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
47 --column c1
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
48 --geneuniverse '$geneuniverse'
f62d29616966 planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents: 1
diff changeset
49 --header None
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
50 #end if
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
51
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
52
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
53
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
54 ]]></command>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
55
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
56 <inputs>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
57 <conditional name="inputtype">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-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.">
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
59 <option value="file_all" selected="true">Input file containing your identifiers</option>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
60 <option value="copy_paste">Copy/paste your list of IDs</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
61 </param>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
62 <when value="copy_paste">
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
63 <param name="genelist" type="text" label="Enter a list of identifiers">
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
64 <sanitizer>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
65 <valid initial="string.printable">
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
66 <remove value="&apos;"/>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
67 </valid>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
68 <mapping initial="none">
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
69 <add source="&apos;" target="__sq__"/>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
70 </mapping>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
71 </sanitizer>
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
72 </param>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
73 </when>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
74 <when value="file_all">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-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."/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-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"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
77
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
78 <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
79 <option value="TRUE" selected="true">Yes</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
80 <option value="FALSE" selected="false">No</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
81 </param>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
82 </when>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
83 </conditional>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
84 <param name="geneuniverse" type="select" label="Select a specie">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
85 <option value="org.At.tair.db" >Arabidopsis</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
86 <option value="org.Ce.eg.db" >C.elegans</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
87 <option value="org.Dm.eg.db" >Fly</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
88 <option value="org.Hs.eg.db" selected="true">Human</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
89 <option value="org.Mm.eg.db" >Mouse</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
90 <option value="org.Sc.sqd.db" >Yeast</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
91 </param>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
92
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
93 <param name="ontocat" type="select" label="Ontology category">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
94 <option value="BP" >Biological Process</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
95 <option value="CC" >Cellular Component</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
96 <option value="MF" >Molecular Function</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
97 </param>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
98
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
99 <param name="option" type="select" label="Choose the topGO option for your analysis">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
100 <option value="classic" >Classic fisher test</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
101 <option value="elim" selected="true">Elim</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
102 <option value="weight01" >Weight01</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
103 <option value="parentchild" >ParentChild</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
104 </param>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-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"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
106 <param name="correction" label="Choose a correction for multiple testing" type="select">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
107 <option value="none" >None</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
108 <option value="holm">Holm correction</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
109 <option value="hochberg" >Hochberg correction</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
110 <option value="hommel" >Hommel correction</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
111 <option value="bonferroni" >Bonferroni correction</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
112 <option value="BH" selected="true">Benjamini and Hochberg</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
113 <option value="BY" >Benjamini and Yekutieli</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
114 <option value="fdr" >FDR</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
115 </param>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
116 <conditional name="condtext">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
117 <param name="textoutput" type="select" label="Generate a text file for results">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
118 <option value="TRUE">Yes</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
119 <option value="FALSE">No</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
120 </param>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
121 <when value="TRUE"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
122 <when value="FALSE"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
123 </conditional>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
124 <conditional name="condbar">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
125 <param name="barplotoutput" type="select" label="Generate a barplot of over-represented GO terms">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
126 <option value="TRUE">Yes</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
127 <option value="FALSE">No</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
128 </param>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
129 <when value="TRUE"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
130 <when value="FALSE"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
131 </conditional>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
132 <conditional name="conddot">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
133 <param name="dotplotoutput" type="select" label="Generate a dotplot of over-represented GO terms">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
134 <option value="TRUE">Yes</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
135 <option value="FALSE">No</option>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
136 </param>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
137 <when value="TRUE"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
138 <when value="FALSE"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
139 </conditional>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
140 </inputs>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
141 <outputs>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
142
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
143 <data name="outputtext" format="tabular" label="Text output for topGO analysis $ontocat category" from_work_dir="result.csv">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
144 <filter>condtext['textoutput']=="TRUE"</filter>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
145 </data>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
146
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
147 <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
148 <filter>condbar['barplotoutput']=="TRUE"</filter>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
149 </data>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
150
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
151 <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
152 <filter>conddot['dotplotoutput']=="TRUE"</filter>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
153 </data>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
154
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
155 </outputs>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
156 <tests>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
157 <test>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
158 <conditional name="inputtype">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
159 <param name="filetype " value="tabfile"/>
1
6788a57c5cb5 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
160 <param name="genelist" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/>
6788a57c5cb5 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
161 <param name="column" value="c8"/>
6788a57c5cb5 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
162 <param name="header" value="TRUE"/>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
163 </conditional>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
164 <param name="ontocat" value="BP"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
165 <param name="option" value="elim"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
166 <param name="threshold" value="1e-3"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
167 <param name="correction" value="BH"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
168 <conditional name="condtext">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
169 <param name="textoutput" value="TRUE"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
170 </conditional>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
171 <conditional name="condbar">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
172 <param name="barplotoutput" value="TRUE"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
173 </conditional>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
174 <conditional name="conddot">
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
175 <param name="dotoutput" value="TRUE"/>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
176 </conditional>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
177 <param name="geneuniverse" value="org.Hs.eg.db"/>
1
6788a57c5cb5 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
178 <output name="outputtext" file="Text_output_for_topGO_analysis_BP_category.tabular"/>
6788a57c5cb5 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
179 <output name="outputbarplot" file="Barplot_output_for_topGO_analysis_BP_category.png"/>
6788a57c5cb5 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
180 <output name="outputdotplot" file="Dotplot_output_for_topGO_analysis_BP_category.png"/>
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
181 </test>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
182 </tests>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
183 <help><![CDATA[
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
184
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
185
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
186 **Galaxy component based on R package topGO.**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
187
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
188 **Input required**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
189
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
190 This component works with Ensembl gene ids (e.g : ENSG0000013618). You can
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
191 copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
192 where there are contained.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
193
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
194 **Principle**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
195
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-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**.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
197
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
198 **Output**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
199
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
200 Three kind of outputs are available : a textual output, a barplot output and
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
201 a dotplot output.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
202
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
203 *Textual output* :
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
204 The text output lists all the GO-terms that were found significant under the specified threshold.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
205
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
206
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
207 The different fields are as follow :
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
208
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
209 - Annotated : number of genes in org.Hs.eg.db which are annotated with the GO-term.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
210
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
211 - Significant : number of genes belonging to your input which are annotated with the GO-term.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
212
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-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.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
214
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
215 - pvalues : pvalue obtained after the test
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
216
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
217 - ( qvalues : additional column with adjusted pvalues )
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
218
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
219
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
220 **Tests**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
221
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-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 :
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
223 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
224
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
225 **Multiple testing corrections**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
226
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
227 Furthermore, the following corrections for multiple testing can also be applied :
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
228
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
229 - holm
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
230
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
231 - hochberg
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
232
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
233 - hommel
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
234
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
235 - bonferroni
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
236
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
237 - BH
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
238
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
239 - BY
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
240
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
241 - fdr
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
242
8
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
243 -----
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
244
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
245 .. class:: infomark
ddaa0c318d65 planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
proteore
parents: 7
diff changeset
246
0
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
247 **Authors**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
248
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
249 Alexa A and Rahnenfuhrer J (2016). topGO: Enrichment Analysis for Gene Ontology. R package version 2.30.0.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
250
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
251 **Galaxy integration**
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
252
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-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
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
254
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
255 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
256
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
257 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
258
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
259 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
260
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
261 ]]></help>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
262 <citations>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
263 </citations>
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
264
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty
proteore
parents:
diff changeset
265 </tool>