Mercurial > repos > proteore > proteore_topgo

annotate topGO.xml @ 13:bb92de0eb880 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 328e16fd172a591be630a80c71288e09bafa8edd-dirty
author proteore
date Thu, 25 Oct 2018 04:37:13 -0400
parents 3d6b76f301c2
children 4ebc0fa10ebd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
bb92de0eb880 planemo upload commit 328e16fd172a591be630a80c71288e09bafa8edd-dirty
proteore
parents: 12
diff changeset
1 <tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2018.10.25">
10
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
2 <description>(Human, Mouse, Rat) (topGO)</description>
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
3 <requirements>
2
02558d6a391c planemo upload commit 0be58bb700f64de6792a7234a11675bae2755e8f-dirty
proteore
parents: 1
diff changeset
4 <requirement type="package" version="3.4.1">R</requirement>
1
5569a3f066cf planemo upload commit dd5bd9c90796d9d9a0f62992bb5ca33b0efe6a05-dirty
proteore
parents: 0
diff changeset
5 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
1
5569a3f066cf planemo upload commit dd5bd9c90796d9d9a0f62992bb5ca33b0efe6a05-dirty
proteore
parents: 0
diff changeset
7 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
5569a3f066cf planemo upload commit dd5bd9c90796d9d9a0f62992bb5ca33b0efe6a05-dirty
proteore
parents: 0
diff changeset
8 <requirement type="package" version="3.5.0">bioconductor-org.ce.eg.db</requirement>
5569a3f066cf planemo upload commit dd5bd9c90796d9d9a0f62992bb5ca33b0efe6a05-dirty
proteore
parents: 0
diff changeset
9 <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement>
5569a3f066cf planemo upload commit dd5bd9c90796d9d9a0f62992bb5ca33b0efe6a05-dirty
proteore
parents: 0
diff changeset
10 <requirement type="package" version="3.5.0">bioconductor-org.sc.sgd.db</requirement>
8
f325701409e6 planemo upload commit 2007526ffd7115f74961cddf477086e43d0726a5
proteore
parents: 7
diff changeset
11 <!--requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement-->
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
12 <requirement type="package" version="1.56.0">bioconductor-graph</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
13 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
14 <requirement type="package" version="3.5.0">bioconductor-go.db</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
15 <requirement type="package" version="2.30.0">bioconductor-topgo</requirement>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
16 </requirements>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
17 <stdio>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
18 <exit_code range="1:" />
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
19 </stdio>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
20 <command><![CDATA[
10
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
21
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
22 Rscript --vanilla $__tool_directory__/topGO_enrichment.R
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
23 --inputtype="$inputtype.filetype"
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
24 --input='$inputtype.genelist'
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
25
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
26 #if $inputtype.filetype == "file"
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
27 --column='$inputtype.column'
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
28 --header='$inputtype.header'
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
29 #end if
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
30
10
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
31 --ontology='$ontocat'
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
32 --option='$option'
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
33 --threshold='$threshold'
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
34 --correction='$correction'
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
35 --textoutput='$textoutput'
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
36 --barplotoutput='$barplot'
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
37 --dotplotoutput='$dotplot'
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
38 --geneuniverse='$geneuniverse'
11
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
39 --background="$background_genes.background"
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
40
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
41 #if $background_genes.background == "true"
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
42 --background_genes="$background_genes.inputtype.genelist"
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
43 --background_input_type="$background_genes.inputtype.filetype"
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
44 #if $background_genes.inputtype.filetype == "file"
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
45 --background_header="$background_genes.inputtype.header"
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
46 --background_column="$background_genes.inputtype.column"
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
47 #end if
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
48 #end if
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
49
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
50 ]]></command>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
51
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
52 <inputs>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
53 <conditional name="inputtype">
13
bb92de0eb880 planemo upload commit 328e16fd172a591be630a80c71288e09bafa8edd-dirty
proteore
parents: 12
diff changeset
54 <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 Converter tool.">
10
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
55 <option value="file" selected="true">Input file containing your identifiers</option>
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
56 <option value="copy_paste">Copy/paste your list of IDs</option>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
57 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
58 <when value="copy_paste">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
59 <param name="genelist" type="text" label="Enter a list of identifiers">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
60 <sanitizer>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
61 <valid initial="string.printable">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
62 <remove value="&apos;"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
63 </valid>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
64 <mapping initial="none">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
65 <add source="&apos;" target="__sq__"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
66 </mapping>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
67 </sanitizer>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
68 </param>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
69 </when>
10
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
70 <when value="file">
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
71 <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."/>
7
8d35400e0325 planemo upload commit 26575daf6b3f9ed4f203b50e10e58933b94a94c5-dirty
proteore
parents: 6
diff changeset
72 <param name="column" type="text" label="Please specify the column where your Ensembl IDs are (e.g : Enter 'c1' for column n°1..)" value="c1"/>
10
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
73 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file have a header?" />
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
74 </when>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
75 </conditional>
11
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
76 <conditional name="background_genes">
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
77 <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Would you like to define your own background IDs"/>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
78 <when value="true">
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
79 <conditional name="inputtype">
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
80 <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.">
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
81 <option value="file" selected="true">Input file containing your identifiers</option>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
82 <option value="copy_paste">Copy/paste your list of IDs</option>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
83 </param>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
84 <when value="copy_paste">
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
85 <param name="genelist" type="text" label="Enter a list of identifiers">
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
86 <sanitizer>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
87 <valid initial="string.printable">
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
88 <remove value="&apos;"/>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
89 </valid>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
90 <mapping initial="none">
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
91 <add source="&apos;" target="__sq__"/>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
92 </mapping>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
93 </sanitizer>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
94 </param>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
95 </when>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
96 <when value="file">
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
97 <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."/>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
98 <param name="column" type="text" label="Please specify the column where your Ensembl IDs are (e.g : Enter 'c1' for column n°1..)" value="c1"/>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
99 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file have a header?" />
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
100 </when>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
101 </conditional>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
102 </when>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
103 <when value="false"/>
ddcc0347c54a planemo upload commit 76a36ad5001b9d90c680ff389c7ab7187a790275-dirty
proteore
parents: 10
diff changeset
104 </conditional>
10
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
105 <param name="geneuniverse" type="select" label="Select a specie">
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
106 <!--option value="org.At.tair.db" >Arabidopsis</option-->
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
107 <option value="org.Ce.eg.db" >Worm (C. elegans)</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
108 <option value="org.Dm.eg.db" >Fly (D. melanogaster)</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
109 <option value="org.Hs.eg.db" selected="true">Human (H. sapiens)</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
110 <option value="org.Mm.eg.db" >Mouse (M. musculus)</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
111 <option value="org.Sc.sgd.db" >Yeast (S. cerevisiae)</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
112 </param>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
113 <param name="ontocat" type="select" label="Ontology category">
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
114 <option value="BP" >Biological Process</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
115 <option value="CC" >Cellular Component</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
116 <option value="MF" >Molecular Function</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
117 </param>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
118 <param name="option" type="select" label="Choose the topGO option for your analysis">
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
119 <option value="classic" >Classic fisher test</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
120 <option value="elim" selected="true">Elim</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
121 <option value="weight01" >Weight01</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
122 <option value="parentchild" >ParentChild</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
123 </param>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
124 <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"/>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
125 <param name="correction" label="Choose a correction for multiple testing" type="select">
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
126 <option value="none" >None</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
127 <option value="holm">Holm correction</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
128 <option value="hochberg" >Hochberg correction</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
129 <option value="hommel" >Hommel correction</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
130 <option value="bonferroni" >Bonferroni correction</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
131 <option value="BH" selected="true">Benjamini and Hochberg</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
132 <option value="BY" >Benjamini and Yekutieli</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
133 <option value="fdr" >FDR</option>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
134 </param>
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
135 <param name="textoutput" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a text file for results" />
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
136 <param name="barplot" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a barplot of over-represented GO terms" />
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
137 <param name="dotplot" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a dotplot of over-represented GO terms" />
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
138 </inputs>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
139 <outputs>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
140
10
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
141 <data name="outputtext" format="tsv" label="Text output for topGO analysis $ontocat category" from_work_dir="result">
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
142 <filter>textoutput</filter>
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
143 </data>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
144
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
145 <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png">
10
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
146 <filter>barplot</filter>
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
147 </data>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
148
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
149 <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png">
10
511b060e9890 planemo upload commit 5733164d8d85e557ef99150193e71221df4ea012-dirty
proteore
parents: 9
diff changeset
150 <filter>dotplot</filter>
0
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
151 </data>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
152
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
153 </outputs>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
154 <tests>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
155 <test>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
156 <conditional name="inputtype">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
157 <param name="filetype " value="tabfile"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
158 <param name="genelist" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
159 <param name="column" value="c8"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
160 <param name="header" value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
161 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
162 <param name="ontocat" value="BP"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
163 <param name="option" value="elim"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
164 <param name="threshold" value="1e-3"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
165 <param name="correction" value="BH"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
166 <conditional name="condtext">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
167 <param name="textoutput" value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
168 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
169 <conditional name="condbar">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
170 <param name="barplotoutput" value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
171 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
172 <conditional name="conddot">
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
173 <param name="dotoutput" value="TRUE"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
174 </conditional>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
175 <param name="geneuniverse" value="org.Hs.eg.db"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
176 <output name="outputtext" file="Text_output_for_topGO_analysis_BP_category.tabular"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
177 <output name="outputbarplot" file="Barplot_output_for_topGO_analysis_BP_category.png"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
178 <output name="outputdotplot" file="Dotplot_output_for_topGO_analysis_BP_category.png"/>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
179 </test>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
180 </tests>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
181 <help><![CDATA[
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
182
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
183
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
184 **Galaxy component based on R package topGO.**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
185
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
186 **Input required**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
187
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
188 This component works with Ensembl gene ids (e.g : ENSG0000013618). You can
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
189 copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab)
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
190 where there are contained.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
191
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
192 **Principle**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
193
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
194 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
195
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
196 **Output**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
197
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
198 Three kind of outputs are available : a textual output, a barplot output and
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
199 a dotplot output.
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
200
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
201 *Textual output* :
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
202 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
203
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
204
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
205 The different fields are as follow :
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
206
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
207 - 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
208
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
209 - 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
210
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
211 - 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
212
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
213 - pvalues : pvalue obtained after the test
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
214
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
215 - ( qvalues : additional column with adjusted pvalues )
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
216
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
217
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
218 **Tests**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
219
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
220 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
221 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
222
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
223 **Multiple testing corrections**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
224
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
225 Furthermore, the following corrections for multiple testing can also be applied :
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
226
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
227 - holm
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
228
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
229 - hochberg
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
230
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
231 - hommel
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
232
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
233 - bonferroni
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
234
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
235 - BH
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
236
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
237 - BY
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
238
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
239 - fdr
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
240
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
241 -----
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
242
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
243 .. class:: infomark
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
244
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
245 **Authors**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
246
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
247 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
248
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
249 **Galaxy integration**
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
250
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
251 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
252
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
253 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
254
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
255 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
256
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
257 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
258
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
259 ]]></help>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
260 <citations>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
261 </citations>
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
262
92dfcfb03add planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
263 </tool>