Mercurial > repos > proteore > proteore_go_terms_profiles_comparison

annotate GO_prof_comp.xml @ 0:a0ea9e00bd66 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
author proteore
date Thu, 28 Feb 2019 05:53:47 -0500
parents
children 41298201a5f9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
1 <tool id="go_terms_profiles_comparison" name="GO terms profiles comparison " version="2019.02.28">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
2 <description>(Human, Mouse, Rat)[clusterProfiler]</description>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
3 <requirements>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
4 <requirement type="package" version="3.4.1">R</requirement>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
7 <requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
8 <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
9 <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
10 </requirements>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
12
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
13 Rscript $__tool_directory__/GO_prof_comp.R
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
14 --inputtype1="$input1.ids1"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
15 --inputtype2="$input2.ids2"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
16
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
17 #if $input1.ids1 == "text"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
18 --input1="$input1.txt1"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
19 #else if $input1.ids1 == "file"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
20 --input1="$input1.file1"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
21 --header1="$input1.header1"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
22 --column1="$input1.ncol1"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
23 #end if
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
24
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
25 --list_name1="$list_name1"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
26
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
27 #if $input2.ids2 == "text"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
28 --input2="$input2.txt2"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
29 #else if $input2.ids2 == "file"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
30 --input2="$input2.file2"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
31 --header2="$input2.header2"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
32 --column2="$input2.ncol2"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
33 #end if
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
34
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
35 --list_name2="$list_name2"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
36 --org="$species"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
37 --ont="$ontology"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
38 --lev="$level"
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
39
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
40 > $log
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
41
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
42 ]]></command>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
43 <inputs>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
44 <conditional name="input1" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
45 <param name="ids1" type="select" label="Enter your Gene ID list" help="Copy/paste or from a file (e.g. table)" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
46 <option value="text">Copy/paste your IDs</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
47 <option value="file" selected="true">Input file containing your IDs</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
48 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
49 <when value="text" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
50 <param name="txt1" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: 2810 7534' >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
51 <sanitizer>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
52 <valid initial="string.printable">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
53 <remove value="&apos;"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
54 </valid>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
55 <mapping initial="none">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
56 <add source="&apos;" target="__sq__"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
57 </mapping>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
58 </sanitizer>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
59 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
60 </when>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
61 <when value="file" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
62 <param name="file1" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
63 <param name="header1" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
64 <param name="ncol1" type="text" value="c1" 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'>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
65 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
66 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
67 </when>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
68 </conditional>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
69 <param name="list_name1" type="text" label="name of your first ids list" value="list1" optional="false">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
70 <sanitizer>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
71 <valid initial="string.printable">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
72 <remove value="&apos;"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
73 </valid>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
74 <mapping initial="none">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
75 <add source="&apos;" target="__sq__"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
76 </mapping>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
77 </sanitizer>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
78 <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
79 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
80 <conditional name="input2" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
81 <param name="ids2" type="select" label="Enter your Gene ID list" help="Copy/paste or from a file (e.g. table)" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
82 <option value="text">Copy/paste your IDs</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
83 <option value="file" selected="true">Input file containing your IDs</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
84 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
85 <when value="text" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
86 <param name="txt2" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: 2810 7534' >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
87 <sanitizer>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
88 <valid initial="string.printable">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
89 <remove value="&apos;"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
90 </valid>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
91 <mapping initial="none">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
92 <add source="&apos;" target="__sq__"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
93 </mapping>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
94 </sanitizer>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
95 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
96 </when>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
97 <when value="file" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
98 <param name="file2" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
99 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
100 <param name="ncol2" type="text" value="c1" 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'>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
101 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
102 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
103 </when>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
104 </conditional>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
105 <param name="list_name2" type="text" label="name of your second ids list" value="list2">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
106 <sanitizer>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
107 <valid initial="string.printable">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
108 <remove value="&apos;"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
109 </valid>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
110 <mapping initial="none">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
111 <add source="&apos;" target="__sq__"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
112 </mapping>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
113 </sanitizer>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
114 <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
115 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
116 <param name="species" type="select" label="Species" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
117 <option value="org.Hs.eg.db">Human (Homo sapiens) </option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
118 <option value="org.Mm.eg.db">Mouse (Mus musculus) </option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
119 <option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
120 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
121 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Select GO terms category" optional="false" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
122 <option value="CC">Cellular Component</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
123 <option value="BP">Biological Process</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
124 <option value="MF">Molecular Function</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
125 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
126 <param name="level" type="select" label="Ontology level (the higher this number, the deeper the GO level)">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
127 <option value="1">1</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
128 <option value="2" >2</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
129 <option value="3" selected="True">3</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
130 <option value="4">4</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
131 <option value="5">5</option>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
132 </param>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
133 </inputs>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
134 <outputs>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
135 <data name="log" format="txt" label="Compare lists" />
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
136 <collection type="list" label="clusterProfiler text files" name="text_output">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
137 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tsv"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
138 </collection>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
139 <collection type="list" label="clusterProfiler diagram outputs" name="graph_output" >
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
140 <discover_datasets pattern="(?P&lt;designation&gt;.+.png)" ext="png" />
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
141 </collection>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
142 </outputs>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
143 <tests>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
144 <test>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
145 <conditional name="input1">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
146 <param name="ids1" value="file"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
147 <param name="file1" value="Bred.tsv"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
148 <param name="header1" value="true"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
149 <param name="ncol1" value="c1"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
150 </conditional>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
151 <conditional name="input2">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
152 <param name="ids2" value="file"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
153 <param name="file2" value="Muc.tsv"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
154 <param name="header2" value="true"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
155 <param name="ncol2" value="c1"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
156 </conditional>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
157 <param name="list_name1" value="Bred"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
158 <param name="list_name2" value="Muc"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
159 <param name="species" value="org.Hs.eg.db"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
160 <param name="ontology" value="BP"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
161 <param name="level" value="3"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
162 <output name="log" file="log.txt" />
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
163 <output_collection name="text_output">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
164 <element name="GO_profiles_comp_BP.tsv" file="GO_profiles_comp_BP.tsv" ftype="tsv"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
165 </output_collection>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
166 <output_collection name="graph_output">
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
167 <element name="GO_profiles_comp_BP.png" file="GO_profiles_comp_BP.png" ftype="png"/>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
168 </output_collection>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
169 </test>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
170 </tests>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
171 <help><![CDATA[
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
172
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
173 **Description**
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
174
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
175 This tool is based on R package clusterProfiler and allows to perform GO terms classification and enrichment analyses on gene/protein sets (e.g. given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene/protein set).
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
176
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
177 Given a list of IDs, this tool:
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
178
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
179 (i) performs gene classification based on GO distribution at a specific level,
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
180
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
181 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, compared to a background. User has the possibility to use background corresponding to the whole organism or to a user-defined list. In this latter case, we recommand to use the "Build tissue-specific expression dataset" ProteoRE tool to create this list according to your need.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
182
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
183 -----
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
184
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
185 **Input**
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
186
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
187 Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) or by copy/pasting your IDs (separated by a space).
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
188
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
189 "Select type/source of IDs": only entrez gene ID (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
190
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
191 -----
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
192
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
193 **Parameters**
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
194
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
195 "Species": the three supported species are Homo sapiens, Mus musculus and Rattus norvegicus
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
196
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
197 "Perform GO categories representation analysis?": classify genes based on their projection at a specific level of the GO corpus (see parameter below), and provides functions (set to "Yes")
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
198
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
199 "Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 3) (set to level "2" by default). In general the higher the level, the more semantically specific the term is.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
200
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
201 "Perform GO categories enrichment analysis?": calculate enrichment test for GO terms based on hypergeometric distribution (set to "Yes")
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
202
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
203 "P-value cut off": P-value threshold value for the declaration of significance (default is < 0.01)
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
204
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
205 "Q-value cut off": to prevent high false discovery rate (FDR) in multiple testing, Q-values (adjusted P-values) are estimated for FDR control. (default is < 0.05)
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
206
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
207 "Define your own background IDs?": by default the whole genome/proteome is used as a reference background to compute the enrichment. As this reference set should normally only include genes/proteins that were monitored during your analysis, this option allows to provide your own background; this could be for instance, the total number of genes/proteins expressed in the tissue/sample under study.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
208
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
209 If you want to use your own background, click on the "Yes" button. Your gene/protein set must be a list of Entrez gene ID or Uniprot accession number (otherwise, use the ID-Converter tool of ProteoRE). Select the file containing your list of ID (as background), then specify the column number which contains IDs and the type of IDs (gene Entrez or Uniprot Accession number) as requested.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
210
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
211 Of note: for Human species, you can build your own background by using the "Build tissue-specific expression dataset" tool of ProteoRE.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
212
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
213 -----
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
214
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
215 **Output**
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
216
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
217 Diagram output: graphical output in the form of bar-plot or dot-plot (png, jpeg or pdf format), one figure for each GO category.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
218 Text tables: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency)d graphics representing the repartition and/or enrichment of GO categories. One table and one graphic will be produced for each GO catagory.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
219
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
220 -----
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
221
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
222 **Authors**
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
223 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
224 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
225
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
226 User manual / Documentation of the clusterProfiler R package (functions and parameters):
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
227 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
228
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
229 -----
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
230
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
231 .. class:: infomark
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
232
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
233 **Galaxy integration**
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
234
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
235 Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
236
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
237 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
238
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
239 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
240
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
241 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
242
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
243
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
244 ]]></help>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
245 <citations>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
246 </citations>
a0ea9e00bd66 planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
proteore
parents:
diff changeset
247 </tool>