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comparison reactome_analysis.xml @ 1:35cd50b8ccf2 draft

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planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
author proteore
date Fri, 16 Feb 2018 03:43:58 -0500
parents 216bd2a75b1d
children 6c84a41c44d8
comparison
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0:216bd2a75b1d 1:35cd50b8ccf2
14 #end if 14 #end if
15 15
16 ]]></command> 16 ]]></command>
17 <inputs> 17 <inputs>
18 <conditional name="opt"> 18 <conditional name="opt">
19 <param name="input" type="select" label="Input identifiers" multiple="False" > 19 <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" >
20 <option value="text">Copy/paste your list of IDs </option> 20 <option value="text">Copy/paste your list of IDs </option>
21 <!--option value="file">Choose a single-column file </option--> 21 <option value="file">Input file containing your identifiers</option>
22 <option value="file">Choose a multiple-columns file </option>
23 </param> 22 </param>
24 <when value="text" > 23 <when value="text" >
25 <param name="list" type="text" label="Enter list of identifiers" /> 24 <param name="list" type="text" label="Enter list of identifiers" />
26 </when> 25 </when>
27 <!--when value="file" >
28 <param name="idfile" type="data" format="txt" label="Choose a single-column file" />
29 </when-->
30 <when value="file" > 26 <when value="file" >
31 <param name="file" type="data" format="txt, tabular" label="Choose a multiple-columns file" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" /> 27 <param name="file" type="data" format="txt, tabular" label="Input file containing your identifiers" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" />
32 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 28 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
33 <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' /> 29 <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' />
34 </when> 30 </when>
35 31
36 </conditional> 32 </conditional>
40 <data name="trash" format="tabular" label="Invalid identifiers" /> 36 <data name="trash" format="tabular" label="Invalid identifiers" />
41 </outputs> 37 </outputs>
42 <tests> 38 <tests>
43 <test> 39 <test>
44 <conditional name="opt" > 40 <conditional name="opt" >
45 <param name="input" value="mq" /> 41 <param name="input" value="file" />
46 <param name="file" value="UnipIDs.txt" /> 42 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
47 <param name="header" value="false" /> 43 <param name="header" value="true" />
48 <param name="ncol" value="c1" /> 44 <param name="ncol" value="c1" />
49 </conditional> 45 </conditional>
50 <output name="output" file="reactome_output.html" ftype="html" /> 46 <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" />
51 <output name="trash" file="reactome_invalide_ids.txt" ftype="tab" /> 47 <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" />
52 </test> 48 </test>
53 </tests> 49 </tests>
54 <help><![CDATA[ 50 <help><![CDATA[
55 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. 51 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.
56 52
57 **For the rows that have more than 1 ID, only the first one is taken into account** 53 **For the rows that have more than 1 ID, only the first one is taken into account**
54 **Supported IDs: Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157), gene name (e.g. AQP7)**
58 55
59 **This tool only accepts letters (a-z or A-Z), numbers (0-9) and 3 characters "." "-" "_" for IDs. If there is ID containing other than these characters, it will be removed from the queue and placed in "Invalid identifiers" file** 56 -----
57
58 .. class:: infomark
59
60 **Authors**
61
62 Fabregat et al. 2017 PMID: 29145629 (https://www.ncbi.nlm.nih.gov/pubmed/29145629)
63
64 Milacic et al. 2012 PMID:24213504 (https://www.ncbi.nlm.nih.gov/pubmed/24243840)
65
66 .. class:: infomark
67
68 **Galaxy integration**
69
70 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
71
72 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform,
73
74 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
60 ]]></help> 75 ]]></help>
61 <citations> 76 <citations>
62 </citations> 77 </citations>
63 </tool> 78 </tool>