Mercurial > repos > proteore > proteore_reactome

comparison reactome_analysis.xml @ 8:a58dc5d4b8cd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
author proteore
date Fri, 28 Jun 2019 05:17:11 -0400
parents 6c95f1b88627
children badc91b93945
comparison
equal deleted inserted replaced
7:6c95f1b88627 8:a58dc5d4b8cd
1 <tool id="reactome_analysis" name="Query pathway database" version="2019.03.05"> 1 <tool id="reactome_analysis" name="Query pathway database" version="2019.06.27">
2 <description>[Reactome]</description> 2 <description>[Reactome]</description>
3 <requirements> 3 <requirements>
4 </requirements> 4 </requirements>
5 <stdio> 5 <stdio>
6 <exit_code range="1:" /> 6 <exit_code range="1:" />
18 --species "$species" 18 --species "$species"
19 19
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <conditional name="opt"> 22 <conditional name="opt">
23 <param name="input" type="select" label="Input IDs (UniProt Accession number, Entrez Gene ID or Gene Name" multiple="False" > 23 <param name="input" type="select" label="Input IDs (UniProt Accession number, Entrez Gene ID, Gene Name)" multiple="False" >
24 <option value="text">Copy/paste your list of IDs </option> 24 <option value="text">Copy/paste your list of IDs </option>
25 <option value="file" selected="true">Input file containing your IDs</option> 25 <option value="file" selected="true">Input file containing your IDs</option>
26 </param> 26 </param>
27 <when value="text" > 27 <when value="text" >
28 <param name="list" type="text" label="Enter list of IDs" help="IDs must be separated by a space into the form field, for example: P31946 P62258"> 28 <param name="list" type="text" label="Enter list of IDs" help="IDs must be separated by a space into the form field, for example: P31946 P62258">
42 <param type="text" name="ncol" value="c1" label="Column number of IDs (e.g : Enter c1 for column n°1)"> 42 <param type="text" name="ncol" value="c1" label="Column number of IDs (e.g : Enter c1 for column n°1)">
43 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> 43 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
44 </param> 44 </param>
45 </when> 45 </when>
46 </conditional> 46 </conditional>
47 <param name="species" type="select" label="Species"> 47 <param name="species" type="select" label="Species (human, mouse, rat)">
48 <option value="48887">Human (Homo sapiens)</option> 48 <option value="48887">Human (Homo sapiens)</option>
49 <option value="48892">Mouse (Mouse musculus)</option> 49 <option value="48892">Mouse (Mouse musculus)</option>
50 <option value="48895">Rat (Rattus norvegicus)</option> 50 <option value="48895">Rat (Rattus norvegicus)</option>
51 </param> 51 </param>
52 </inputs> 52 </inputs>
80 80
81 A list of gene/protein IDs. List of IDs can be entered either in a copy/paste manner or by selecting a file with your IDs. 81 A list of gene/protein IDs. List of IDs can be entered either in a copy/paste manner or by selecting a file with your IDs.
82 82
83 ID types allowed are: UniProt accNumber (e.g. O75391), Entrez gene ID (e.g. 8086) and gene name (e.g. TP53, NUP58...). If you have other type of ID, please use the ID_Converter tool of ProteoRE. 83 ID types allowed are: UniProt accNumber (e.g. O75391), Entrez gene ID (e.g. 8086) and gene name (e.g. TP53, NUP58...). If you have other type of ID, please use the ID_Converter tool of ProteoRE.
84 84
85 .. class:: warningmark
86
87 In copy/paste mode, the number of IDs considered in input is limited to 5000.
88
85 ----- 89 -----
86 90
87 **Parameters** 91 **Parameters**
88 92
89 "Select species": can be Human (Homo sapiens), Mouse (Mouse musculus) or Rat (Rattus norvegicus) 93 "Select species": can be Human (Homo sapiens), Mouse (Mouse musculus) or Rat (Rattus norvegicus)
106 110
107 .. class:: infomark 111 .. class:: infomark
108 112
109 **Galaxy integration** 113 **Galaxy integration**
110 114
111 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 115 Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
112 116
113 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 117 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
114 118
115 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 119 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
116 120
117 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 121 Help: contact@proteore.org for any questions or concerns about this tool.
118 ]]></help> 122 ]]></help>
119 <citations> 123 <citations>
120 </citations> 124 </citations>
121 </tool> 125 </tool>