Mercurial > repos > proteore > proteore_kegg_pathways_coverage

comparison compute_kegg_pathways.xml @ 2:179bfc3c7938 draft

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planemo upload commit 170560760f17fd1b77efe8bb95fedf3eb2433f0b-dirty
author proteore
date Thu, 22 Nov 2018 04:38:42 -0500
parents 7004924a3686
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1:7004924a3686 2:179bfc3c7938
1 <tool id="compute_kegg_pathways" name="KEGG pathways" version="2018.11.14"> 1 <tool id="compute_kegg_pathways" name="KEGG pathways" version="2018.11.22">
2 <description>identification and coverage</description> 2 <description>identification and coverage</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> 4 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
20 --species="$species" 20 --species="$species"
21 21
22 ]]></command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <conditional name="input" > 24 <conditional name="input" >
25 <param name="ids" type="select" label="Enter your identifiers (KEGG genes ID)" help="Copy/paste or ID list from a file (e.g. table)" > 25 <param name="ids" type="select" label="Enter your list of identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
26 <option value="text">Copy/paste your identifiers</option> 26 <option value="text">Copy/paste your identifiers</option>
27 <option value="file" selected="true">Input file containing your KEGG genes IDs</option> 27 <option value="file" selected="true">Input file containing your identifiers</option>
28 </param> 28 </param>
29 <when value="text" > 29 <when value="text" >
30 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab,space or carriage return into the form field, for example: hsa:3306 hsa:22948' > 30 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab, space or carriage return into the form field, for example: hsa:3306 hsa:22948' >
31 <sanitizer invalid_char=''> 31 <sanitizer invalid_char=''>
32 <valid initial="string.printable"> 32 <valid initial="string.printable">
33 <remove value="&apos;"/> 33 <remove value="&apos;"/>
34 </valid> 34 </valid>
35 <mapping initial="none"> 35 <mapping initial="none">
37 </mapping> 37 </mapping>
38 </sanitizer> 38 </sanitizer>
39 </param> 39 </param>
40 </when> 40 </when>
41 <when value="file" > 41 <when value="file" >
42 <param name="file" type="data" format="txt,tabular,tsv" label="Select a file that contains your list of KEGG gene IDs" help="" /> 42 <param name="file" type="data" format="txt,tabular,tsv" label="Select a file that contains your list of identifiers" help="" />
43 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 43 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain a header?" />
44 <param name="ncol" type="text" value="c1" label="The column number of KEGG genes 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' /> 44 <param name="ncol" type="text" value="c1" label="The column number of your identifiers to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
45 </when> 45 </when>
46 </conditional> 46 </conditional>
47 <param name="id_type" type="select" label="select your identifiers type :"> 47 <param name="id_type" type="select" label="select your identifiers type :" >
48 <option value="ncbi-geneid" selected="true">Entrez gene ID</option> 48 <option value="ncbi-geneid" selected="true">Entrez genes ID</option>
49 <option value="kegg-id">KEGG ID (genes)</option> 49 <option value="kegg-id">KEGG genes ID</option>
50 <option value="uniprot">Uniprot Accession number</option> 50 <option value="uniprot">Uniprot Accession number</option>
51 51
52 </param> 52 </param>
53 <param name="species" type="select" label="Select species"> 53 <param name="species" type="select" label="Select species">
54 <option value="hsa">Human (H. sapiens)</option> 54 <option value="hsa">Human (H. sapiens)</option>
74 <output name="output1" value="test.tsv" /> 74 <output name="output1" value="test.tsv" />
75 </test> 75 </test>
76 </tests> 76 </tests>
77 <help><![CDATA[ 77 <help><![CDATA[
78 78
79 This tool maps a list of KEGG gene IDs to KEGG pathway and return a list of KEGG pathways ranked by the percentage of coverage for each pathway; this is done by computing the number of KEGG genes IDs from your list divided by the total number of KEGG genes present in the considered species for each KEGG pathway. 79 This tool maps a list of identifiers to KEGG pathway and return a list of KEGG pathways ranked by the percentage of coverage for each pathway. This is done by computing the number of KEGG genes IDs from your list divided by the total number of KEGG genes present in the considered species for each KEGG pathway.
80 80
81 It allows you to directly identify the signaling pathways that are the most covered by your proteomics dataset. 81 It allows you to directly identify the signaling pathways that are the most covered by your proteomics dataset.
82 82
83 By default the number of pathway to be displayed is set to 10 and sorted in descending order. 83 By default the number of pathway to be displayed is set to 10 and sorted in descending order.
84 84