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comparison cluster_profiler.xml @ 0:bd052861852b draft

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