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comparison reactome_analysis.xml @ 5:34097acf457c draft

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planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
author proteore
date Thu, 27 Jun 2019 04:21:19 -0400
parents 113cce3fc379
children eb051cba2bda
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4:113cce3fc379 5:34097acf457c
1 <tool id="reactome_analysis" name="Query Reactome pathway database" version="2018.12.12"> 1 <tool id="reactome_analysis" name="Query pathway database" version="2019.06.27">
2 <description></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:" />
7 </stdio> 7 </stdio>
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 identifiers (Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157) or gene name (e.g. AQP7)" 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 identifiers</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 identifiers" help="IDs must be separated by 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">
29 <sanitizer> 29 <sanitizer>
30 <valid initial="string.printable"> 30 <valid initial="string.printable">
31 <remove value="&apos;"/> 31 <remove value="&apos;"/>
32 </valid> 32 </valid>
33 <mapping initial="none"> 33 <mapping initial="none">
35 </mapping> 35 </mapping>
36 </sanitizer> 36 </sanitizer>
37 </param> 37 </param>
38 </when> 38 </when>
39 <when value="file" > 39 <when value="file" >
40 <param name="file" type="data" format="txt, tabular" label="Input file containing your identifiers" help="Input file is a tab-delimited file with at least one contain containing identifier" /> 40 <param name="file" type="data" format="txt, tabular" label="Input file containing your IDs" help="Input file is a tab-delimited file with at least one contain containing identifier" />
41 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 41 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
42 <param type="text" name="ncol" value="c1" label="Please specify the column number where are your 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>
44 </param>
43 </when> 45 </when>
44 </conditional> 46 </conditional>
45 <param name="species" type="select" label="Select species"> 47 <param name="species" type="select" label="Species (human, mouse, rat)">
46 <option value="48887">Human (H. sapiens)</option> 48 <option value="48887">Human (Homo sapiens)</option>
47 <option value="48892">Mouse (M. musculus)</option> 49 <option value="48892">Mouse (Mouse musculus)</option>
48 <option value="48895">Rat (R. norvegicus)</option> 50 <option value="48895">Rat (Rattus norvegicus)</option>
49 </param> 51 </param>
50 </inputs> 52 </inputs>
51 <outputs> 53 <outputs>
52 <data name="output" format="html" label="" /> 54 <data name="output" format="html" label="" />
53 <data name="trash" format="tabular" hidden="true" label="Invalid id not send to reactome"> 55 <data name="trash" format="tabular" hidden="true" label="Invalid id not send to reactome">
65 <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" /> 67 <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" />
66 <!-- <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" hidden="true" /> --> 68 <!-- <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" hidden="true" /> -->
67 </test> 69 </test>
68 </tests> 70 </tests>
69 <help><![CDATA[ 71 <help><![CDATA[
70 Reactome software provides service of creating diagram representing the relations between the biological processes. This tool allows linking to Reactome web service with pre-loaded data from a list of IDs, a file containing IDs or from a column of a complexed file.
71 72
72 **For the rows that have more than 1 ID, only the first one is taken into account.** 73 **Description**
73 74
74 **Supported IDs: Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157), gene name (e.g. AQP7). If there is any ID containing invalid characters, it will be removed from the queue and placed in "Invalid identifiers" file.** 75 This tool allows to map your gene/protein list to the Reactome pathway browser (visualize and interact with biological pathways) via a web service with pre-loaded data from your list of IDs
75 76
76 **Supported species: Human (H. sapiens), Mouse (M. musculus), Rat (Rattus norvegicus)** 77 -----
78
79 **Input**
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.
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.
84
85 .. class:: warningmark
86
87 In copy/paste mode, the number of IDs considered in input is limited to 5000.
88
89 -----
90
91 **Parameters**
92
93 "Select species": can be Human (Homo sapiens), Mouse (Mouse musculus) or Rat (Rattus norvegicus)
94
95 -----
96
97 **Output**
98
99 To access results, click on the "View data" icon (from the item created in your history panel), then click on the "Analyze" button in the central panel will directly display the results in the Reactome pathway browser.
77 100
78 ----- 101 -----
79 102
80 .. class:: infomark 103 .. class:: infomark
81 104
82 **Authors** 105 **Authors**
83 106
84 Fabregat et al. 2017 PMID: 29145629 (https://www.ncbi.nlm.nih.gov/pubmed/29145629) 107 Fabregat et al., The Reactome Pathway Knowledgebase. Nucleic Acids Res. 2018. 46(D1):D649-D655. doi: 10.1093/nar/gkx1132. PubMed PMID: 29145629
85 108
86 Milacic et al. 2012 PMID:24213504 (https://www.ncbi.nlm.nih.gov/pubmed/24243840) 109 -----
87 110
88 .. class:: infomark 111 .. class:: infomark
89 112
90 **Galaxy integration** 113 **Galaxy integration**
91 114
92 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
93 116
94 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform, 117 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
95 118
96 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 119 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
120
121 Help: contact@proteore.org for any questions or concerns about this tool.
97 ]]></help> 122 ]]></help>
98 <citations> 123 <citations>
99 </citations> 124 </citations>
100 </tool> 125 </tool>