Mercurial > repos > proteore > proteore_goprofiles

comparison goprofiles.xml @ 8:386145573c19 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b
author proteore
date Tue, 18 Dec 2018 09:54:57 -0500
parents 6afe8166a9a4
children 948fecb6a40b
comparison
equal deleted inserted replaced
7:3e138d54c105 8:386145573c19
1 <tool id="goProfiles" name="goProfiles" version="2018.09.21"> 1 <tool id="goProfiles" name="Statistical analysis of functional profiles" version="2018.12.12">
2 <description>Statistical analysis of functional profiles</description> 2 <description>(Human, Mouse) [goProfiles]</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.4.1">R</requirement> 4 <requirement type="package" version="3.4.1">R</requirement>
5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> 5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> 6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
7 <!--requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement-->
7 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement> 8 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
8 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement> 9 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
9 <requirement type="package" version="1.38.0">goprofiles</requirement> 10 <requirement type="package" version="1.38.0">goprofiles</requirement>
10 </requirements> 11 </requirements>
11 <stdio> 12 <stdio>
22 --ncol="$input.ncol" 23 --ncol="$input.ncol"
23 --header="$input.header" 24 --header="$input.header"
24 #end if 25 #end if
25 26
26 --id_type="$input.id_type" 27 --id_type="$input.id_type"
27
28 --onto_opt="$onto_opt" 28 --onto_opt="$onto_opt"
29 29 --plot_opt="$plot_opt"
30 --plot_opt="$opt.plot_opt"
31
32 --level="$level" 30 --level="$level"
33
34 --per="$per" 31 --per="$per"
35
36 --title="$title" 32 --title="$title"
37
38 --duplicate="$duplicate" 33 --duplicate="$duplicate"
39
40 --text_output="$text_output" 34 --text_output="$text_output"
41 35 --species="$species" > $log
42 --species="$species"
43 36
44 ]]></command> 37 ]]></command>
45 <inputs> 38 <inputs>
46 <conditional name="input" > 39 <conditional name="input" >
47 <param name="ids" type="select" label="Enter your ID list (only Entrez Gene ID or UniProt accession number allowed" help="Copy/paste or ID list from a file (e.g. table)" > 40 <param name="ids" type="select" label="Enter your IDs (Entrez Gene ID or UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" >
48 <option value="text">Copy/paste your identifiers</option> 41 <option value="text">Copy/paste your IDs</option>
49 <option value="file" selected="true">Input file containing your identifiers</option> 42 <option value="file" selected="true">Input file containing your IDs</option>
50 </param> 43 </param>
51 <when value="text" > 44 <when value="text" >
52 <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 <param name="text" type="text" label="Copy/paste your IDs" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
53 <sanitizer> 46 <sanitizer>
54 <valid initial="string.printable"> 47 <valid initial="string.printable">
55 <remove value="&apos;"/> 48 <remove value="&apos;"/>
56 </valid> 49 </valid>
57 <mapping initial="none"> 50 <mapping initial="none">
58 <add source="&apos;" target="__sq__"/> 51 <add source="&apos;" target="__sq__"/>
59 </mapping> 52 </mapping>
60 </sanitizer> 53 </sanitizer>
61 </param> 54 </param>
62 <param name="id_type" type="select" label="Please select the type of your IDs list" > 55 <param name="id_type" type="select" label="Select type of IDs list" >
63 <option value="Entrez">Entrez Gene ID</option> 56 <option value="Entrez">Entrez Gene ID</option>
64 <option value="UniProt">UniProt protein acession number</option> 57 <option value="UniProt">UniProt Accession number</option>
65 </param> 58 </param>
66 </when> 59 </when>
67 <when value="file" > 60 <when value="file" >
68 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" /> 61 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
69 <param name="ncol" type="text" value="c1" 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="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' />
70 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 63 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
71 <param name="id_type" type="select" label="Please select the type of your IDs list" > 64 <param name="id_type" type="select" label="Select type of IDs list" >
72 <option value="Entrez">Entrez Gene ID</option> 65 <option value="Entrez">Entrez Gene ID</option>
73 <option value="UniProt">UniProt protein ID</option> 66 <option value="UniProt">Uniprot Accession number</option>
74 </param> 67 </param>
75 </when> 68 </when>
76 </conditional> 69 </conditional>
77 <param name="duplicate" type="boolean" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" /> 70 <param name="duplicate" type="boolean" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
78 <param name="species" type="select" label="Select your species"> 71 <param name="species" type="select" label="Species">
79 <option value="org.Hs.eg.db">Human (Homo sapiens)</option> 72 <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
80 <option value="org.Mm.eg.db">Mouse (Mus musculus)</option> 73 <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>
74 <!--option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option-->
81 </param> 75 </param>
82 <param type="select" name="onto_opt" label="Please select GO terms category" multiple="True" display="checkboxes" > 76 <param type="select" name="onto_opt" label="Select GO terms category" multiple="True" display="checkboxes" optional="false" >
83 <option value="CC">Cellular Component (CC)</option> 77 <option value="CC">Cellular Component (CC)</option>
84 <option value="MF">Molecular Function (MF)</option> 78 <option value="MF">Molecular Function (MF)</option>
85 <option value="BP">Biological Process (BP)</option> 79 <option value="BP">Biological Process (BP)</option>
86 </param> 80 </param>
87 <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)" > 81 <param type="select" name="level" label="Ontology level (the higher this number, the deeper the GO level)" >
88 <option value="1">1</option> 82 <option value="1">1</option>
89 <option value="2" selected="True">2</option> 83 <option value="2" selected="True">2</option>
90 <option value="3">3</option> 84 <option value="3">3</option>
91 </param> 85 </param>
92 <param type="boolean" name="per" label="Plot absolute or relative frequencies (not summing to 100)" truevalue="TRUE" falsevalue="FALSE" /> 86 <param type="boolean" name="per" label="Plot absolute frequencies?" truevalue="TRUE" falsevalue="FALSE" />
93 <param type="text" name="title" label="Enter title of your figure" /> 87 <param type="text" name="title" label="Enter title of your figure" />
94 <section name="opt" title="Choose graphical output (bar plots) format: png, jpeg, pdf" expanded="False" help="By default, PDF is chosen as output format"> 88 <param type="select" name="plot_opt" label="Plot file format">
95 <param type="select" name="plot_opt" label="Choose plot output extension" multiple="True" display="checkboxes" > 89 <option value="PNG">png</option>
96 <option value="PNG">PNG</option> 90 <option value="JPEG">jpeg</option>
97 <option value="JPEG">JPEG</option> 91 <option value="PDF" selected="True">pdf</option>
98 <option value="PDF" selected="True">PDF</option> 92 </param>
99 </param> 93
100 </section>
101 </inputs> 94 </inputs>
102 <outputs> 95 <outputs>
103 <collection type="list" label="GO Profile diagram output" name="output" > 96 <data name="log" format="tsv" label="goProfiles log" />
97 <collection type="list" label="goProfiles text files" name="text_output">
98 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tsv"/>
99 </collection>
100 <collection type="list" label="goProfiles diagram output" name="output" >
104 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" /> 101 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" />
105 <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" /> 102 <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" />
106 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" /> 103 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" />
107 </collection> 104 </collection>
108 <data name="text_output" format="tabular" label="GO Profile text output" />
109 </outputs> 105 </outputs>
110 <tests> 106 <tests>
111 <test> 107 <test>
112 <conditional name="input"> 108 <conditional name="input">
113 <param name="ids" value="file" /> 109 <param name="ids" value="file" />
119 <param name="duplicate" value="false"/> 115 <param name="duplicate" value="false"/>
120 <param name="onto_opt" value="CC,MF,BP" /> 116 <param name="onto_opt" value="CC,MF,BP" />
121 <param name="level" value="2" /> 117 <param name="level" value="2" />
122 <param name="per" value="true" /> 118 <param name="per" value="true" />
123 <param name="title" value="Test" /> 119 <param name="title" value="Test" />
124 <section name="opt" > 120 <param name="plot_opt" value="PDF" />
125 <param name="plot_opt" value="PDF" />
126 </section>
127 <output_collection name="output" type="list" > 121 <output_collection name="output" type="list" >
128 <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/> 122 <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/>
129 <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/> 123 <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/>
130 <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/> 124 <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/>
131 </output_collection> 125 </output_collection>
132 <output name="text_output" file="GO_Profile_text_output.txt"/> 126 <output name="log" file="GO_Profile_text_output.tsv"/>
133 </test> 127 </test>
134 </tests> 128 </tests>
135 <help><![CDATA[ 129 <help><![CDATA[
136 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 accession number) as input.
137 130
138 You can choose one or more GO categories: 131 **Description**
139 132
140 * Biological Process (BP) 133 This tool is based on the goProfiles R package; it performs statistical analysis of functional profiles based on Gene Ontology (GO). Functional profile at a given GO level is obtained by counting the
141 * Cellular Component (CC) 134 number of identifiers having a hit in each category of this level.
142 * Molecular Function (MF)
143 135
144 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; textual output with GO terms and their computed frequencies is also provided. 136 -----
145 137
146 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) 138 **Input**
147 139
148 If your type of identifiers is not supported (i.e. different from Uniprot and Entrez), please use the **ID Converter** tool in the ProteoRE section to convert your list of IDs first. 140 Two modes are allowed: either by copy/pasting your IDs (separated by a space) or by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers).
141 Only entrez gene ID (e.g : 4151) 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.
142
143 -----
144
145 **Parameters**
146
147 "Species": enter the sepcies you are working on; Homo sapiens and Mus musculus supported (Rattus norvegicus coming soon)
148
149 "Select GO terms category": you can choose one or more GO categories which are Biological Process (BP), Cellular Component (CC) and Molecular Function (MF)
150
151 "Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 3). In general the higher the level, the more semantically specific the term is.
152
153 -----
154
155 **Ouput**
156
157 Diagram output: graphical output in the form of bar-plot or dot-plot (png, jpeg or pdf format), one figure for each GO category.
158
159 text output: 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)
149 160
150 ----- 161 -----
151 162
152 .. class:: infomark 163 .. class:: infomark
153 164
154 **Authors** 165 **Authors**
155 166
156 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. 167 Salicrú M, Ocaña J, Sánchez-Pla A. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011. 12:401. doi:10.1186/1471-2105-12-401. PubMed PMID: 21999355
168
169 -----
157 170
158 .. class:: infomark 171 .. class:: infomark
159 172
160 **Galaxy integration** 173 **Galaxy integration**
161 174
162 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 175 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
163 176
164 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform, 177 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform, FR
178
179 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
165 180
166 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 181 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
167 182
168 ]]></help> 183 ]]></help>
169 <citations> 184 <citations>