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comparison goprofiles.xml @ 9:948fecb6a40b draft

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planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty
author proteore
date Mon, 04 Mar 2019 05:48:48 -0500
parents 386145573c19
children 2138e0035e57
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8:386145573c19 9:948fecb6a40b
1 <tool id="goProfiles" name="Statistical analysis of functional profiles" version="2018.12.12"> 1 <tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.02.27">
2 <description>(Human, Mouse) [goProfiles]</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="3.5.0">bioconductor-org.rn.eg.db</requirement-->
8 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement> 8 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
9 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement> 9 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
10 <requirement type="package" version="1.38.0">goprofiles</requirement> 10 <requirement type="package" version="1.38.0">goprofiles</requirement>
11
11 </requirements> 12 </requirements>
12 <stdio> 13 <stdio>
13 <exit_code range="1:" /> 14 <exit_code range="1:" />
14 </stdio> 15 </stdio>
15 <command><![CDATA[ 16 <command><![CDATA[
57 <option value="UniProt">UniProt Accession number</option> 58 <option value="UniProt">UniProt Accession number</option>
58 </param> 59 </param>
59 </when> 60 </when>
60 <when value="file" > 61 <when value="file" >
61 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> 62 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
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' /> 63 <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'>
64 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
65 </param>
63 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 66 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
64 <param name="id_type" type="select" label="Select type of IDs list" > 67 <param name="id_type" type="select" label="Select type of IDs list" >
65 <option value="Entrez">Entrez Gene ID</option> 68 <option value="Entrez">Entrez Gene ID</option>
66 <option value="UniProt">Uniprot Accession number</option> 69 <option value="UniProt">Uniprot Accession number</option>
67 </param> 70 </param>
80 </param> 83 </param>
81 <param type="select" name="level" label="Ontology level (the higher this number, the deeper the GO level)" > 84 <param type="select" name="level" label="Ontology level (the higher this number, the deeper the GO level)" >
82 <option value="1">1</option> 85 <option value="1">1</option>
83 <option value="2" selected="True">2</option> 86 <option value="2" selected="True">2</option>
84 <option value="3">3</option> 87 <option value="3">3</option>
88 <option value="4">4</option>
89 <option value="5">5</option>
90 <option value="6">6</option>
85 </param> 91 </param>
86 <param type="boolean" name="per" label="Plot absolute frequencies?" truevalue="TRUE" falsevalue="FALSE" /> 92 <param type="boolean" name="per" label="Plot absolute frequencies?" truevalue="TRUE" falsevalue="FALSE" />
87 <param type="text" name="title" label="Enter title of your figure" /> 93 <param type="text" name="title" label="Enter title of your figure">
94 <sanitizer invalid_char=''>
95 <valid initial="string.printable">
96 <remove value="&apos;"/>
97 <remove value="/"/>
98 </valid>
99 <mapping>
100 <add source="&#x20;" target=""/>
101 </mapping>
102 </sanitizer>
103 </param>
88 <param type="select" name="plot_opt" label="Plot file format"> 104 <param type="select" name="plot_opt" label="Plot file format">
89 <option value="PNG">png</option> 105 <option value="PNG" selected="True">png</option>
90 <option value="JPEG">jpeg</option> 106 <option value="JPEG">jpeg</option>
91 <option value="PDF" selected="True">pdf</option> 107 <option value="PDF">pdf</option>
92 </param> 108 </param>
93 109
94 </inputs> 110 </inputs>
95 <outputs> 111 <outputs>
96 <data name="log" format="tsv" label="goProfiles log" /> 112 <data name="log" format="tsv" label="goProfiles log" />
146 162
147 "Species": enter the sepcies you are working on; Homo sapiens and Mus musculus supported (Rattus norvegicus coming soon) 163 "Species": enter the sepcies you are working on; Homo sapiens and Mus musculus supported (Rattus norvegicus coming soon)
148 164
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) 165 "Select GO terms category": you can choose one or more GO categories which are Biological Process (BP), Cellular Component (CC) and Molecular Function (MF)
150 166
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. 167 "Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 6). In general the higher the level, the more semantically specific the term is.
152 168
153 ----- 169 -----
154 170
155 **Ouput** 171 **Ouput**
156 172
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. 173 Diagram output: graphical output in the form of bar-plot or dot-plot (png (default format), jpeg or pdf format), one figure for each GO category.
158 174
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) 175 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)
160 176
161 ----- 177 -----
162 178