annotate cluster_profiler.xml @ 0:bd052861852b draft

planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
author proteore
date Thu, 01 Mar 2018 10:05:18 -0500
parents
children 09ba28df72ad
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
1 <tool id="cluter_profiler" name="clusterProfiler Enrichment Analysis" version="0.1.0">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
2 <requirements>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
3 <requirement type="package" version="3.4.1">R</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
4 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
5 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
6 <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
7 <requirement type="package" version="3.0.5">bioconductor-clusterprofiler</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
8 </requirements>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
10 Rscript "$__tool_directory__/GO-enrich.R"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
11 #if $input.ids == "text"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
12 --input_type="text"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
13 --input="$input.text"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
14 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
15 --input_type="file"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
16 --input="$input.file"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
17 --ncol="$input.ncol"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
18 --header="$input.header"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
19 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
20
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
21 --id_type="$idti.idtypein"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
22
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
23 --species="$species"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
24
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
25 #if $ggo.go_represent == "true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
26 --go_represent="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
27 --level="$ggo.level"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
28 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
29 --go_represent="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
30 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
31
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
32 #if $ego.go_enrich == "true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
33 --go_enrich="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
34 --pval_cutoff="$ego.pval"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
35 --qval_cutoff="$ego.qval"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
36 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
37 --go_enrich="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
38 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
39
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
40 --onto_opt="$ontology"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
41
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
42 --text_output="$text_output"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
43 ]]></command>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
44 <inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
45 <conditional name="input" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
46 <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
47 <option value="text">Copy/paste your identifiers</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
48 <option value="file">Input file containing your identifiers</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
49 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
50 <when value="text" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
51 <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
52 <sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
53 <valid initial="string.printable">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
54 <remove value="&apos;"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
55 </valid>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
56 <mapping initial="none">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
57 <add source="&apos;" target="__sq__"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
58 </mapping>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
59 </sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
60 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
61 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
62 <when value="file" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
63 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
64 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
65 <param name="ncol" type="text" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
66 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
67 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
68 <conditional name="idti" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
69 <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
70 <option value="Uniprot">UniProt accession number</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
71 <option value="Entrez">Entrez Gene ID</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
72 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
73 <when value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
74 <when value="Entrez"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
75 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
76 <param name="species" type="select" label="Select a species" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
77 <option value="human">Human</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
78 <option value="mouse">Mouse</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
79 <option value="rat">Rat</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
80 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
81 <conditional name="ggo">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
82 <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories representation analysis?"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
83 <when value="true">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
84 <param name="level" type="select" label="Level of the ontology at which the profile has to be built (the higher this number, the deeper the GO level)">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
85 <option value="1">1</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
86 <option value="2">2</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
87 <option value="3" selected="True">3</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
88 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
89 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
90 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
91 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
92 <conditional name="ego">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
93 <param name="go_enrich" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories enrichment analysis?"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
94 <when value="true">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
95 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
96 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
97 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
98 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
99 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
100 <!--conditional name="fun" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
101 <param name="go_function" type="select" display="checkboxes" multiple="true" label="Please select analyses to perform">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
102 <option value="ggo">GO categories representation</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
103 <option value="ego">GO categories enrichment (compared to a background/reference)</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
104 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
105 <when value="ggo" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
106 <param name="level" type="select" label="Level of the ontology at which the profile has to be built (the higher this number, the deeper the GO level)">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
107 <option value="1">1</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
108 <option value="2">2</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
109 <option value="3" selected="True">3</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
110 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
111 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
112 <when value="ego" >
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"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
115 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
116 </conditional-->
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
117
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
118 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
119 <option value="CC">Cellular Component</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
120 <option value="BP">Biological Process</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
121 <option value="MF">Molecular Function</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
122 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
123
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
124
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
125
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
126 </inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
127 <outputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
128 <data name="text_output" format="tabular" label="clusterProfiler text output" />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
129 <collection type="list" label="clusterProfiler diagram outputs" name="output" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
130 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
131 </collection>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
132 </outputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
133 <tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
134 <test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
135 <conditional name="input">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
136 <param name="ids" value="file"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
137 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
138 <param name="header" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
139 <param name="ncol" value="c1"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
140 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
141 <conditional name="idti">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
142 <param name="idtypein" value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
143 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
144 <param name="species" value="human"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
145 <conditional name="ggo">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
146 <param name="go_represent" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
147 <param name="level" value="3"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
148 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
149 <conditional name="ego">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
150 <param name="go_enrich" value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
151 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
152 <param name="ontology" value="CC"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
153 <output name="text_output" file="clusterProfiler_text_output.tabular"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
154 <output_collection name="output">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
155 <element name="clusterProfiler_diagram_outputs__GGO.CC.png" file="clusterProfiler_diagram_outputs__GGO.CC.png" ftype="png"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
156 </output_collection>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
157 </test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
158 </tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
159 <help><![CDATA[
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
160
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
161 **Galaxy component based on R package clusterProfiler (see ref below)**
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
162
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
163 This component allows to perform GO enrichment-analyses.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
164 Given a list of IDs, the tool either
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
165 (i) performs gene classification based on GO distribution at a specific level, or
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
166 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list,
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
167 compared to a background (whole organism or user-defined list).
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
168
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
169 **Input required**
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
170
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
171 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946).
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
172 You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
173
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
174
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
175 **Output**
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
176
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
177 Text (tables) and graphics representing the repartition and/or enrichment of GO categories.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
178
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
179 **User manual / Documentation** of the clusterProfiler R package (functions and parameters):
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
180 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
181 (Very well explained)
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
182
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
183 **Reference**
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
184
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
185 clusterProfiler R package reference :
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
186 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
187 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
188 doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
189
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
190
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
191 **Galaxy integration**
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
192
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
193 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
194
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
195 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
196
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
197 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
198
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
199 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
200
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
201
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
202 ]]></help>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
203 <citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
204 </citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
diff changeset
205 </tool>