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1 <tool id="goProfiles" name="goProfiles" version="0.1.0">
2 <description> Identify enriched biological themes, GO terms from your protein list.
3 </description>
4 <requirements>
5 <requirement type="package" version="3.4.1">R</requirement>
6 <requirement type="package" version="3.3.0">bioconductor-org.hs.eg.db</requirement>
7 <requirement type="package" version="1.38.0">bioconductor-annotationdbi</requirement>
8 <requirement type="package" version="2.34.0">bioconductor-biobase</requirement>
9 <requirement type="package" version="1.38.0">goprofiles</requirement>
10 </requirements>
11 <stdio>
12 <exit_code range="1:" />
13 </stdio>
14 <command><![CDATA[
15 Rscript $__tool_directory__/goprofiles.R
16 #if $input.ids == "text"
17 "$input.text" "text"
18 #else
19 "$input.file,$input.ncol,$input.header" "file"
20 #end if
21
22 $input.id_type
23
24 $onto_opt
25
26 $opt.plot_opt
27
28 $level
29
30 $per
31
32 "$title"
33
34 $duplicate
35
36 ]]></command>
37 <inputs>
38 <conditional name="input" >
39 <param name="ids" type="select" label="Provide your Entrez Gene or UniProt identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
40 <option value="text">Copy/paste your identifiers</option>
41 <option value="file">Input file containing your identifiers</option>
42 </param>
43 <when value="text" >
44 <param name="text" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
45 <sanitizer>
46 <valid initial="string.printable">
47 <remove value="&apos;"/>
48 </valid>
49 <mapping initial="none">
50 <add source="&apos;" target="__sq__"/>
51 </mapping>
52 </sanitizer>
53 </param>
54 <param name="id_type" type="select" label="Please select the type of your IDs list" >
55 <option value="Entrez">Entrez Gene ID</option>
56 <option value="UniProt">UniProt protein ID</option>
57 </param>
58 </when>
59 <when value="file" >
60 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
61 <param name="ncol" type="text" label="The column number of IDs to use" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
62 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
63 <param name="id_type" type="select" label="Please select the type of your IDs list" >
64 <option value="Entrez">Entrez Gene ID</option>
65 <option value="UniProt">UniProt protein ID</option>
66 </param>
67 </when>
68 </conditional>
69 <param name="duplicate" type="boolean" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
70 <param type="select" name="onto_opt" label="Please select GO terms category" multiple="True" display="checkboxes" >
71 <option value="CC">Cellular Component (CC)</option>
72 <option value="MF">Molecular Function (MF)</option>
73 <option value="BP">Biological Process (BP)</option>
74 </param>
75 <param type="select" name="level" label="Level of the ontology at which the profile has to be built (the higher this number, the deeper the GO level)" >
76 <option value="1">1</option>
77 <option value="2" selected="True">2</option>
78 <option value="3">3</option>
79 </param>
80 <param type="boolean" name="per" label="Plot absolute or relative frequencies (not summing to 100)" truevalue="TRUE" falsevalue="FALSE" />
81 <param type="text" name="title" label="Enter title of your figure" />
82 <section name="opt" title="Choose graphical output (bar plots) format: png, jpeg, pdf" expanded="False" help="By default, PDF is chosen as output format">
83 <param type="select" name="plot_opt" label="Choose plot output extension" multiple="True" display="checkboxes" >
84 <option value="PNG">PNG</option>
85 <option value="JPEG">JPEG</option>
86 <option value="PDF" selected="True">PDF</option>
87 </param>
88 </section>
89 </inputs>
90 <outputs>
91 <collection type="list" label="GO Profile diagram outputs" name="output" >
92 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" />
93 <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" />
94 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" />
95 </collection>
96 </outputs>
97 <tests>
98 <test>
99 <conditional name="input">
100 <param name="ids" value="file" />
101 <param name="file" value="UnipIDs.txt" />
102 <param name="ncol" value="c1" />
103 <param name="header" value="false" />
104 <param name="id_type" value="UniProt" />
105 </conditional>
106 <param name="onto_opt" value="CC,MF,BP" />
107 <param name="level" value="2" />
108 <param name="per" value="true" />
109 <param name="title" value="Test" />
110 <section name="opt" >
111 <param name="plot_opt" value="PDF" />
112 </section>
113 <output_collection name="output" type="list" >
114 <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" />
115 <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" />
116 <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" />
117 </output_collection>
118 </test>
119 </tests>
120 <help><![CDATA[
121 This tool, based on the goProfiles R package, performs statistical analysis of functional profiles. It is based on GO ontology and considers either a gene set ('Entrez’ Identifiers) or a protein set (Uniprot ID) as input.
122
123 You can choose one or more GO categories:
124
125 * Biological Process (BP)
126 * Cellular Component (CC)
127 * Molecular Function (MF)
128
129 Functional profile at a given GO level is obtained by counting the number of identifiers having a hit in each category of this level (2 by default). Results are displayed as bar plots (with absolute or relative frequencies) and can be exported in pdf, png and jpeg formats.
130
131 For more details about GoProfiles, please read: Salicrú et al. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011;12:401.(https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-401)
132
133 If your type of identifiers is not supported (i.e. different form Uniprot and Entrez), please use the **ID Converter** component in the ProteoRE section to convert your list of IDs first.
134
135 -----
136
137 .. class:: infomark
138
139 **Authors**
140
141 Sanchez A, Ocana J and Salicru M (2016). goProfiles: goProfiles: an R package for the statistical analysis of functional profiles. R package version 1.38.0.
142
143 .. class:: infomark
144
145 **Galaxy integration**
146
147 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
148
149 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform,
150
151 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
152
153 ]]></help>
154 <citations>
155 </citations>
156 </tool>