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<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.0">
    
    <description>Create a summary of XCMS analysis</description>
    
    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="1.44.0">xcms</requirement>
        <requirement type="package" version="1.22.0">camera</requirement>
    </requirements>
    
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    
    <command interpreter="Rscript"><![CDATA[
        xcms_summary.r

        image $image 
        htmlOutput $htmlOutput
        user_email $__user_email__
       
    ]]></command>
    
    <inputs>

        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" />

    </inputs>
    
    <outputs>
        <data name="htmlOutput" format="html" label="xcms summary html" />
    </outputs>
    
    <tests>
        <test>
            <param name="image" value="fillpeaks.RData" />
            <output name="htmlOutput" file="summary.html" />
        </test>
    </tests>
    
    <help><![CDATA[

.. class:: infomark

**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff part of Workflow4Metabolomics.org [W4M]

 | Contact [e-mail] for any questions or concerns about the Galaxy implementation of this tool.

---------------------------------------------------

============
Xcms.summary
============

-----------
Description
-----------

This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools 


---------------------------------------------------

Changelog/News
--------------

**Version 1.0.0 - 10/02/2016**

- NEW: Create a summary of XCMS analysis


    ]]></help>


    <citations>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </citations>

</tool>