<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.4_1">r-snow</requirement>
            <requirement type="package" version="1.0">r-probmetab</requirement>
            <requirement type="package" version="1.1_4">r-batch</requirement>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1" level="fatal" />
        </stdio>
    </xml>

    <token name="@COMMAND_CAMERA_SCRIPT@">
        LANG=C Rscript $__tool_directory__/probmetab.r
    </token>
    
    <!-- zipfile load for planemo test -->
    <token name="@COMMAND_ZIPFILE_LOAD@">
        #if $zipfile_load_conditional.zipfile_load_select == "yes":
            #if $zipfile_load_conditional.zip_file:
                zipfile $zipfile_load_conditional.zip_file
            #end if
        #end if    
    </token>
    <xml name="zipfile_load">
        <conditional name="zipfile_load_conditional">
            <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." >
                <option value="no" >no need</option>
                <option value="yes" selected="peakgroups">yes</option>
            </param>
            <when value="no">
            </when>
            <when value="yes">
                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
            </when>
        </conditional>
    </xml>
    
    <token name="@HELP_AUTHORS@">
.. class:: infomark

**Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br

 | If you use this tool, please cite: Silva RR and al.(2010). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics..
 | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/

.. class:: infomark

**Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff.

 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.

.. class:: infomark

**Contributors**  Ricardo R. Silva rsilvabioinfo@usp.br, Yann Guitton yann.guitton@univ-nantes.fr and Jean-François Martin jean-francois.martin@toulouse.inra.fr

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

    </token>


    <xml name="citation">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btu019</citation>
            <citation type="doi">10.1093/bioinformatics/btu813</citation>
        </citations>
    </xml>
</macros>