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comparison kegg_identification.xml @ 5:6d0ae897d1ca draft

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planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
author proteore
date Thu, 27 Jun 2019 04:19:58 -0400
parents dc39f12f96d1
children 042254fb1f8d
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4:dc39f12f96d1 5:6d0ae897d1ca
1 <tool id="kegg_identification" name="Pathways identification" version="2019.03.05.1"> 1 <tool id="kegg_identification" name="Pathways identification" version="2019.06.27">
2 <description>and coverage [KEGG]</description> 2 <description>and coverage [KEGG]</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 IDs (Entrez gene IDs, KEGG gene IDs or UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" > 25 <param name="ids" type="select" label="Enter your IDs (Entrez gene IDs, KEGG IDs, UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" >
26 <option value="text">Copy/paste your IDs</option> 26 <option value="text">Copy/paste your IDs</option>
27 <option value="file" selected="true">Input file containing your IDs</option> 27 <option value="file" selected="true">Input file containing your IDs</option>
28 </param> 28 </param>
29 <when value="text" > 29 <when value="text" >
30 <param name="txt" type="text" label="Copy/paste your IDs" 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 IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: hsa:3306 hsa:22948' >
91 Input can be either a list of IDs or a file containing multiple columns but with at least one column of IDs (e.g. hsa:04970). 91 Input can be either a list of IDs or a file containing multiple columns but with at least one column of IDs (e.g. hsa:04970).
92 Input IDs type can be Entrez gene ID (e.g. 2243), KEGG gene ID (e.g. hsa:2243 in homo sapiens) or Uniprot accession number (e.g. P02671). 92 Input IDs type can be Entrez gene ID (e.g. 2243), KEGG gene ID (e.g. hsa:2243 in homo sapiens) or Uniprot accession number (e.g. P02671).
93 93
94 .. class:: warningmark 94 .. class:: warningmark
95 95
96 If you use Uniprot accession number, it will be converted to KEGG gene ID; this step can be time consuming. 96 If you use Uniprot accession number, it will be converted to KEGG gene ID; this step can be time consuming. KEGG database being "gene-centric" we recommend the use of Entrez gene IDs.
97 97
98 If your input file contains other type of ID, please use the ID_Converter tool. 98 If your input file contains other type of ID (than those allowed), please use the ID_Converter tool.
99
100 In copy/paste mode, the number of IDs considered in input is limited to 5000.
99 101
100 ----- 102 -----
101 103
102 **Parameters** 104 **Parameters**
103 105
131 133
132 .. class:: infomark 134 .. class:: infomark
133 135
134 **Galaxy integration** 136 **Galaxy integration**
135 137
136 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 138 David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
137 139
138 Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 140 Sandra Dérozier, Olivier Rué, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
139 141
140 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 142 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
141 143
142 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 144 Help: contact@proteore.org for any questions or concerns about this tool.
143 145
144 ]]></help> 146 ]]></help>
145 <citations> 147 <citations>
146 <citation type="bibtex"> 148 <citation type="bibtex">
147 @misc{githubKEGGREST, 149 @misc{githubKEGGREST,