<tool id="reactome_analysis" name="Pathway enrichment analysis" version="2021.04.20">
    <description>[Reactome]</description>
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[

        python $__tool_directory__/reactome_analysis.py 
        #if $opt.input == "text"
        --json "$opt.list" "list" 
        #else if $opt.input == "file"
        --json "$opt.file" "file" "$opt.header" "$opt.ncol" 
        #end if
        --output "$output" 
        --trash "$trash"
        --species "$species"
        
    ]]></command>
    <inputs>
        <conditional name="opt">
            <param name="input" type="select" label="Input IDs (UniProt Accession number, Entrez Gene ID, Gene Name)" multiple="False" >
                <option value="text">Copy/paste your list of IDs </option>
		        <option value="file" selected="true">Input file containing your IDs</option>
            </param>
            <when value="text" >
                <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">
                    <sanitizer>
                        <valid initial="string.printable">
                            <remove value="&apos;"/>
                        </valid>
                        <mapping initial="none">
                            <add source="&apos;" target="__sq__"/>
                        </mapping>
                    </sanitizer>
                </param>
            </when>
            <when value="file" >
                <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" />
                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
		        <param type="text" name="ncol" value="c1" label="Column number of IDs (e.g : Enter c1 for column n°1)">
                    <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
                </param>
            </when>
        </conditional>
        <param name="species" type="select" label="Species (human, mouse, rat)">
            <option value="48887">Human (Homo sapiens)</option>
            <option value="48892">Mouse (Mouse musculus)</option>
            <option value="48895">Rat (Rattus norvegicus)</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="html" label="" />
        <data name="trash" format="tabular" hidden="true" label="Invalid id not send to reactome">
            <discover_datasets pattern="(Reactome_Analysis_Tools_invalid_ID).txt" ext="tabular" visible="false" assign_primary_output="false"/>
        </data>
    </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="tabular"  />
        </test>
    </tests>
    <help><![CDATA[

**Description**

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

-----

**Input** 

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. 

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.

.. class:: warningmark
	
In copy/paste mode, the number of IDs considered in input is limited to 5000.

-----

**Parameters**

"Select species": can be Human (Homo sapiens), Mouse (Mouse musculus) or Rat (Rattus norvegicus)

-----

**Output**

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.  

-----

.. class:: infomark

**Authors** 

Fabregat et al., The Reactome Pathway Knowledgebase. Nucleic Acids Res. 2018. 46(D1):D649-D655. doi: 10.1093/nar/gkx1132. PubMed PMID: 29145629

-----

.. class:: infomark

**Galaxy integration**

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, FR

This work has been partially funded through the French National Agency for Research (ANR) IFB project.

Help: contact@proteore.org for any questions or concerns about this tool.
    ]]></help>
    <citations>
    </citations>
</tool>