<tool id="reactome_analysis" name="Reactome Analysis Tools" version="0.1.0">
    <description>query Reactome with your IDs list
    </description>
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        #if $opt.input == "text"
            python $__tool_directory__/reactome_analysis.py --json "$opt.list" "list" --output "$output" --trash "$trash"
        #else if $opt.input == "file"
            python $__tool_directory__/reactome_analysis.py --json "$opt.file" "file" $opt.header $opt.ncol --output "$output" --trash "$trash"
        #end if
        
    ]]></command>
    <inputs>
        <conditional name="opt">
            <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" >
                <option value="text">Copy/paste your list of IDs </option>
		        <option value="file">Input file containing your identifiers</option>
            </param>
            <when value="text" >
                <param name="list" type="text" label="Enter list of identifiers" />
            </when>
            <when value="file" >
                <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" />
                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
		        <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' />
            </when>
            
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="html" label="" />
        <data name="trash" format="tabular" label="Invalid identifiers" />
    </outputs>
    <tests>
        <test>
            <conditional name="opt" >
                <param name="input" value="file" />
                <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
                <param name="header" value="true" />
                <param name="ncol" value="c1" />
            </conditional>
            <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" />
            <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" />
        </test>
    </tests>
    <help><![CDATA[
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.

**For the rows that have more than 1 ID, only the first one is taken into account**
**Supported IDs: Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157), gene name (e.g. AQP7)**

-----

.. class:: infomark

**Authors** 

Fabregat et al. 2017 PMID: 29145629 (https://www.ncbi.nlm.nih.gov/pubmed/29145629)

Milacic et al. 2012 PMID:24213504 (https://www.ncbi.nlm.nih.gov/pubmed/24243840)

.. class:: infomark

**Galaxy integration**

T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR

Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform,

Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
    ]]></help>
    <citations>
    </citations>
</tool>