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annotate reactome_analysis.xml @ 1:35cd50b8ccf2 draft

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author proteore
date Fri, 16 Feb 2018 03:43:58 -0500
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1 <tool id="reactome_analysis" name="Reactome Analysis Tools" version="0.1.0">
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2 <description>query Reactome with your IDs list
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3 </description>
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4 <requirements>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 #if $opt.input == "text"
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11 python $__tool_directory__/reactome_analysis.py --json "$opt.list" "list" --output "$output" --trash "$trash"
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12 #else if $opt.input == "file"
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13 python $__tool_directory__/reactome_analysis.py --json "$opt.file" "file" $opt.header $opt.ncol --output "$output" --trash "$trash"
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14 #end if
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15
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16 ]]></command>
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17 <inputs>
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18 <conditional name="opt">
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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" >
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20 <option value="text">Copy/paste your list of IDs </option>
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21 <option value="file">Input file containing your identifiers</option>
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22 </param>
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23 <when value="text" >
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24 <param name="list" type="text" label="Enter list of identifiers" />
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25 </when>
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26 <when value="file" >
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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" />
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28 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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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' />
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30 </when>
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31
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32 </conditional>
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33 </inputs>
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34 <outputs>
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35 <data name="output" format="html" label="" />
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36 <data name="trash" format="tabular" label="Invalid identifiers" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <conditional name="opt" >
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41 <param name="input" value="file" />
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42 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
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43 <param name="header" value="true" />
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44 <param name="ncol" value="c1" />
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45 </conditional>
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46 <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" />
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47 <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" />
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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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.
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52
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53 **For the rows that have more than 1 ID, only the first one is taken into account**
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54 **Supported IDs: Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157), gene name (e.g. AQP7)**
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55
1
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56 -----
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57
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58 .. class:: infomark
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59
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60 **Authors**
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61
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62 Fabregat et al. 2017 PMID: 29145629 (https://www.ncbi.nlm.nih.gov/pubmed/29145629)
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63
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64 Milacic et al. 2012 PMID:24213504 (https://www.ncbi.nlm.nih.gov/pubmed/24243840)
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65
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66 .. class:: infomark
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67
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68 **Galaxy integration**
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69
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70 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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71
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72 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform,
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73
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74 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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75 ]]></help>
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76 <citations>
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77 </citations>
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78 </tool>