annotate cluster_profiler.xml @ 8:b29255864039 draft

planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty
author proteore
date Fri, 21 Dec 2018 04:12:32 -0500
parents 4609346d8108
children 2f67202ffdb3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
b29255864039 planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty
proteore
parents: 7
diff changeset
1 <tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.21">
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
2 <description>(Human, Mouse, Rat)[clusterProfiler]</description>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
3 <requirements>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
4 <requirement type="package" version="3.4.1">R</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
7 <requirement type="package" version="3.5.0">bioconductor-org.Rn.eg.db</requirement>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
8 <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
1
09ba28df72ad planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents: 0
diff changeset
9 <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
10 </requirements>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
12 Rscript "$__tool_directory__/GO-enrich.R"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
13 #if $input.ids == "text"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
14 --input_type="text"
4
710414ebb6db planemo upload commit 0a42c3d46be24406936ca0036bb436e6e2524fd2-dirty
proteore
parents: 3
diff changeset
15 --input="$input.txt"
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
16 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
17 --input_type="file"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
18 --input="$input.file"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
19 --ncol="$input.ncol"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
20 --header="$input.header"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
21 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
22
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
23 --id_type="$idti.idtypein"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
24
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
25 --species="$species"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
26
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
27 #if $ggo.go_represent == "true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
28 --go_represent="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
29 --level="$ggo.level"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
30 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
31 --go_represent="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
32 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
33
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
34 #if $ego.go_enrich == "true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
35 --go_enrich="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
36 --pval_cutoff="$ego.pval"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
37 --qval_cutoff="$ego.qval"
6
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
38 #if $ego.universe.universe_option == "true"
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
39 #if $ego.universe.universe_input.universe_ids == "text"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
40 --universe_type="text"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
41 --universe="$ego.universe.universe_input.txt"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
42 #else
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
43 --universe_type="file"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
44 --universe="$ego.universe.universe_input.file"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
45 --uncol="$ego.universe.universe_input.ncol"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
46 --uheader="$ego.universe.universe_input.header"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
47 #end if
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
48 --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
6
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
49 #end if
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
50 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
51 --go_enrich="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
52 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
53
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
54 --plot="$ego.plot"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
55 --onto_opt="$ontology" > $log
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
56 ]]></command>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
57 <inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
58 <conditional name="input" >
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
59 <param name="ids" type="select" label="Enter your IDs (UniProt Accession numer or Gene ID)" help="Copy/paste or from a file (e.g. table)" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
60 <option value="text">Copy/paste your IDs</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
61 <option value="file" selected="true">Input file containing your IDs</option>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
62 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
63 <when value="text" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
64 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
65 <sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
66 <valid initial="string.printable">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
67 <remove value="&apos;"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
68 </valid>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
69 <mapping initial="none">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
70 <add source="&apos;" target="__sq__"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
71 </mapping>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
72 </sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
73 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
74 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
75 <when value="file" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
76 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
77 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
78 <param name="ncol" 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' />
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
79 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
80 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
81 <conditional name="idti" >
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
82 <param name="idtypein" type="select" label="Select type/source of IDs" help="" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
83 <option value="Uniprot">UniProt accession number (e.g.:P31946)</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
84 <option value="Entrez">Entrez Gene ID (e.g.:4151)</option>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
85 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
86 <when value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
87 <when value="Entrez"/>
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
88 </conditional>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
89 <param name="species" type="select" label="Species" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
90 <option value="org.Hs.eg.db">Human (Homo sapiens) </option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
91 <option value="org.Mm.eg.db">Mouse (Mus musculus) </option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
92 <option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
93 </param>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
94 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Select GO terms category" optional="false" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
95 <option value="CC">Cellular Component</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
96 <option value="BP">Biological Process</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
97 <option value="MF">Molecular Function</option>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
98 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
99 <conditional name="ggo">
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
100 <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories representation analysis?"/>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
101 <when value="true">
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
102 <param name="level" type="select" label="Ontology level (the higher this number, the deeper the GO level)">
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
103 <option value="1">1</option>
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
104 <option value="2" selected="True">2</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
105 <option value="3">3</option>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
106 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
107 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
108 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
109 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
110 <conditional name="ego">
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
111 <param name="go_enrich" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories enrichment analysis?"/>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
112 <when value="true">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
113 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
114 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
6
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
115 <conditional name="universe" >
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
116 <param name="universe_option" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs?"/>
6
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
117 <when value="true">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
118 <conditional name="universe_input">
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
119 <param name="universe_ids" type="select" label="Enter your background IDs (UniProt Accession number or Entrez Gene ID)" help="Copy/paste or from a file (e.g. table)" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
120 <option value="text">Copy/paste your background IDs</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
121 <option value="file" selected="true">Input file containing your background IDs</option>
6
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
122 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
123 <when value="text" >
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
124 <param name="txt" type="text" label="Copy/paste your background IDs" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
6
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
125 <sanitizer>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
126 <valid initial="string.printable">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
127 <remove value="&apos;"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
128 </valid>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
129 <mapping initial="none">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
130 <add source="&apos;" target="__sq__"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
131 </mapping>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
132 </sanitizer>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
133 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
134 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
135 <when value="file" >
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
136 <param name="file" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help="" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
137 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
138 <param name="ncol" 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' />
6
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
139 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
140 </conditional>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
141 <conditional name="universe_idti" >
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
142 <param name="universe_idtypein" type="select" label="Select type of background IDs" help="" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
143 <option value="Uniprot">UniProt Accession number</option>
6
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
144 <option value="Entrez">Entrez Gene ID</option>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
145 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
146 <when value="Uniprot"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
147 <when value="Entrez"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
148 </conditional>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
149 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
150 <when value="false"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
proteore
parents: 5
diff changeset
151 </conditional>
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
152 <param name="plot" type="select" display="checkboxes" multiple="true" label="Graphical display" optional="false">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
153 <option selected = "true" value="dotplot">dot-plot</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
154 <option value="barplot">bar-plot</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
155 </param>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
156 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
157 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
158 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
159 </inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
160 <outputs>
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
161 <data name="log" format="tsv" label="Cluster profiler" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
162 <collection type="list" label="clusterProfiler text files" name="text_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
163 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tsv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
164 </collection>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
165 <collection type="list" label="clusterProfiler diagram outputs" name="graph_output" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
166 <discover_datasets pattern="(?P&lt;designation&gt;.+plot)" ext="png" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
167 </collection>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
168 </outputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
169 <tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
170 <test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
171 <conditional name="input">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
172 <param name="ids" value="file"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
173 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
174 <param name="header" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
175 <param name="ncol" value="c1"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
176 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
177 <conditional name="idti">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
178 <param name="idtypein" value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
179 </conditional>
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
180 <param name="species" value="org.Hs.eg.db"/>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
181 <conditional name="ggo">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
182 <param name="go_represent" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
183 <param name="level" value="3"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
184 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
185 <conditional name="ego">
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
186 <param name="go_enrich" value="true"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
187 <conditional name="universe_input">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
188 <param name="universe_ids" value="file"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
189 <param name="file" value="background_ids.txt"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
190 <param name="header" value="true"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
191 <param name="ncol" value="c7"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
192 </conditional>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
193 <conditional name="universe_idti" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
194 <param name="universe_idtypein" value="Uniprot"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
195 </conditional>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
196 </conditional>
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
197 <param name="ontology" value="CC,BP,MF"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
198 <param name="plot" value="dotplot,barplot"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
199 <output name="log" file="log.txt" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
200 <output_collection name="text_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
201 <element name="cluster_profiler_GGO_CC.csv" file="cluster_profiler_GGO_CC.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
202 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_GGO_BP.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
203 <element name="cluster_profiler_GGO_MF.csv" file="cluster_profiler_GGO_MF.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
204 <element name="cluster_profiler_EGO_CC.csv" file="cluster_profiler_EGO_CC.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
205 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_EGO_BP.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
206 <element name="cluster_profiler_EGO_MF.csv" file="cluster_profiler_EGO_MF.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
207 </output_collection>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
208 <output_collection name="graph_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
209 <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
210 <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
211 <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
212 <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
213 <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
214 <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
215 <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png"/>
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
216 </output_collection>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
217 </test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
218 </tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
219 <help><![CDATA[
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
220
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
221 **Description**
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
222
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
223 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).
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
224
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
225 Given a list of IDs, this tool:
5
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
226
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
227 (i) performs gene classification based on GO distribution at a specific level,
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
228
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
229 (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.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
230
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
231 -----
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
232
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
233 **Input**
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
234
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
235 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).
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
236
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
237 "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.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
238
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
239 -----
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
240
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
241 **Parameters**
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
242
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
243 "Species": the three supported species are Homo sapiens, Mus musculus and Rattus norvegicus
1
09ba28df72ad planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents: 0
diff changeset
244
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
245 "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")
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
246
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
247 "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.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
248
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
249 "Perform GO categories enrichment analysis?": calculate enrichment test for GO terms based on hypergeometric distribution (set to "Yes")
5
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
250
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
251 "P-value cut off": P-value threshold value for the declaration of significance (default is < 0.01)
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
252
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
253 "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)
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
254
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
255 "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.
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
256
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
257 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.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
258
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
259 Of note: for Human species, you can build your own background by using the "Build tissue-specific expression dataset" tool of ProteoRE.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
260
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
261 -----
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
262
5
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
263 **Output**
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
264
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
265 Diagram output: graphical output in the form of bar-plot or dot-plot (png, jpeg or pdf format), one figure for each GO category.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
266 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.
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
267
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
268 -----
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
269
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
270 **Authors**
5
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
271 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
272 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)
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
273
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
274 User manual / Documentation of the clusterProfiler R package (functions and parameters):
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
275 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
276
5
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
277 -----
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
278
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
279 .. class:: infomark
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
280
5
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
281 **Galaxy integration**
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
282
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
283 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
284
7
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 6
diff changeset
285 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
286
5
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
287 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
288
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
proteore
parents: 4
diff changeset
289 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
290
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
291
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
292 ]]></help>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
293 <citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
294 </citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
295 </tool>