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comparison goprofiles.xml @ 1:1236ee08ccb8 draft

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planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
author proteore
date Fri, 16 Feb 2018 03:40:36 -0500
parents d89c09253c8d
children 58a8ddd58dde
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0:d89c09253c8d 1:1236ee08ccb8
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.4.1">R</requirement> 5 <requirement type="package" version="3.4.1">R</requirement>
6 <requirement type="package" version="3.3.0">bioconductor-org.hs.eg.db</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> 7 <requirement type="package" version="1.38.0">bioconductor-annotationdbi</requirement>
8 <requirement type="package" version="2.34.0">bioconductor-biobase</requirement> 8 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
9 <requirement type="package" version="1.38.0">goprofiles</requirement> 9 <requirement type="package" version="1.38.0">goprofiles</requirement>
10 </requirements> 10 </requirements>
11 <stdio> 11 <stdio>
12 <exit_code range="1:" /> 12 <exit_code range="1:" />
13 </stdio> 13 </stdio>
14 <command><![CDATA[ 14 <command><![CDATA[
15 Rscript $__tool_directory__/goprofiles.R 15 Rscript $__tool_directory__/goprofiles.R
16 #if $input.ids == "text" 16 #if $input.ids == "text"
17 "$input.text" "text" 17 --input_type="text"
18 #else 18 --input="$input.text"
19 "$input.file,$input.ncol,$input.header" "file" 19 #else
20 --input_type="file"
21 --input="$input.file"
22 --ncol="$input.ncol"
23 --header="$input.header"
20 #end if 24 #end if
21 25
22 $input.id_type 26 --id_type="$input.id_type"
23 27
24 $onto_opt 28 --onto_opt="$onto_opt"
25 29
26 $opt.plot_opt 30 --plot_opt="$opt.plot_opt"
27 31
28 $level 32 --level="$level"
29 33
30 $per 34 --per="$per"
31 35
32 "$title" 36 --title="$title"
33 37
34 $duplicate 38 --duplicate="$duplicate"
39
40 --text_output="$text_output"
35 41
36 ]]></command> 42 ]]></command>
37 <inputs> 43 <inputs>
38 <conditional name="input" > 44 <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)" > 45 <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 <option value="text">Copy/paste your identifiers</option> 46 <option value="text">Copy/paste your identifiers</option>
41 <option value="file">Input file containing your identifiers</option> 47 <option value="file">Input file containing your identifiers</option>
42 </param> 48 </param>
43 <when value="text" > 49 <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' > 50 <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' >
51 </mapping> 57 </mapping>
52 </sanitizer> 58 </sanitizer>
53 </param> 59 </param>
54 <param name="id_type" type="select" label="Please select the type of your IDs list" > 60 <param name="id_type" type="select" label="Please select the type of your IDs list" >
55 <option value="Entrez">Entrez Gene ID</option> 61 <option value="Entrez">Entrez Gene ID</option>
56 <option value="UniProt">UniProt protein ID</option> 62 <option value="UniProt">UniProt protein acession number</option>
57 </param> 63 </param>
58 </when> 64 </when>
59 <when value="file" > 65 <when value="file" >
60 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" /> 66 <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' /> 67 <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' />
91 <collection type="list" label="GO Profile diagram outputs" name="output" > 97 <collection type="list" label="GO Profile diagram outputs" name="output" >
92 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" /> 98 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" />
93 <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" /> 99 <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" />
94 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" /> 100 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" />
95 </collection> 101 </collection>
102 <data name="text_output" format="tabular" label="GO Profile text output" />
96 </outputs> 103 </outputs>
97 <tests> 104 <tests>
98 <test> 105 <test>
99 <conditional name="input"> 106 <conditional name="input">
100 <param name="ids" value="file" /> 107 <param name="ids" value="file" />
101 <param name="file" value="UnipIDs.txt" /> 108 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
102 <param name="ncol" value="c1" /> 109 <param name="ncol" value="c1" />
103 <param name="header" value="false" /> 110 <param name="header" value="talse" />
104 <param name="id_type" value="UniProt" /> 111 <param name="id_type" value="UniProt" />
105 </conditional> 112 </conditional>
113 <param name="duplicate" value="false"/>
106 <param name="onto_opt" value="CC,MF,BP" /> 114 <param name="onto_opt" value="CC,MF,BP" />
107 <param name="level" value="2" /> 115 <param name="level" value="2" />
108 <param name="per" value="true" /> 116 <param name="per" value="true" />
109 <param name="title" value="Test" /> 117 <param name="title" value="Test" />
110 <section name="opt" > 118 <section name="opt" >
111 <param name="plot_opt" value="PDF" /> 119 <param name="plot_opt" value="PDF" />
112 </section> 120 </section>
113 <output_collection name="output" type="list" > 121 <output_collection name="output" type="list" >
114 <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" /> 122 <element name="GO_Profile_diagram_outputs__profile.BP.pdf" file="GO_Profile_diagram_outputs__profile.BP.pdf" ftype="pdf" />
115 <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" /> 123 <element name="GO_Profile_diagram_outputs__profile.CC.pdf" file="GO_Profile_diagram_outputs__profile.CC.pdf" ftype="pdf" />
116 <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" /> 124 <element name="GO_Profile_diagram_outputs__profile.MF.pdf" file="GO_Profile_diagram_outputs__profile.MF.pdf" ftype="pdf" />
117 </output_collection> 125 </output_collection>
126 <output name="text_output" file="GO_Profile_text_output.txt"/>
118 </test> 127 </test>
119 </tests> 128 </tests>
120 <help><![CDATA[ 129 <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. 130 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.
122 131
123 You can choose one or more GO categories: 132 You can choose one or more GO categories:
124 133
125 * Biological Process (BP) 134 * Biological Process (BP)
126 * Cellular Component (CC) 135 * Cellular Component (CC)
127 * Molecular Function (MF) 136 * Molecular Function (MF)
128 137
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. 138 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.
130 139
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) 140 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)
132 141
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. 142 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.
134 143
135 ----- 144 -----
136 145
137 .. class:: infomark 146 .. class:: infomark
138 147