Mercurial > repos > proteore > proteore_kegg_pathways_coverage

comparison compute_kegg_pathways.xml @ 1:7004924a3686 draft

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planemo upload commit 2e8375a0a037aaf4042cdeb5244228d3f9ca583b-dirty
author proteore
date Wed, 14 Nov 2018 05:46:35 -0500
parents 8883a7173cba
children 179bfc3c7938
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0:8883a7173cba 1:7004924a3686
1 <tool id="compute_kegg_pathways" name="KEGG pathways" version="2018.11.12"> 1 <tool id="compute_kegg_pathways" name="KEGG pathways" version="2018.11.14">
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[
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 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 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' />
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="kegg-id">KEGG ID (genes)</option> 49 <option value="kegg-id">KEGG ID (genes)</option>
49 <!--option value="uniprot">Uniprot Accession number</option--> 50 <option value="uniprot">Uniprot Accession number</option>
50 <option value="ncbi-geneid">Entrez gene ID</option> 51
51 </param> 52 </param>
52 <param name="species" type="select" label="Select species"> 53 <param name="species" type="select" label="Select species">
53 <option value="hsa">Human (H. sapiens)</option> 54 <option value="hsa">Human (H. sapiens)</option>
54 <option value="mmu">Mouse (M. musculus)</option> 55 <option value="mmu">Mouse (M. musculus)</option>
55 <option value="rno">Rat (R. norvegicus)</option> 56 <option value="rno">Rat (R. norvegicus)</option>
83 84
84 At the moment three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus). 85 At the moment three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus).
85 86
86 **Input:** 87 **Input:**
87 88
88 Input can be either a list of KEGG genes IDs or a file containing multiple columns but with at least one column of KEGG genes IDs (e.g. hsa04970). If your input file contains other type of IDs, please use the ID_Converter tool to get KEGG genes ID. 89 Input can be either a list of ids or a file containing multiple columns but with at least one column of ids (e.g. hsa04970).
90 Input ids type can be Entrez gene ID, KEGG gene ID or Uniprot accession number.
91
92 .. class:: warningmark
93
94 If you use Uniprot accession number, it will be converted to KEGG gene ID, this step can be time consuming.
95 If your input file contains other type of ids, please use the ID_Converter tool.
89 96
90 **Output:** 97 **Output:**
91 98
92 The output is a tabular file (.tsv) with the following columns: 99 The output is a tabular file (.tsv) with the following columns:
93 100