<?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>

    <token name="@COMMAND_LOG_EXIT@">
        ;
        return=\$?;
        cat 'log.txt';
        sh -c "exit \$return"
    </token>

    <!-- raw file load for planemo test -->
    <token name="@COMMAND_FILE_LOAD_NEUTRAL@">
        #if $file_load_section_selected.file_load_conditional.file_load_select == "yes":
            #if $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("netcdf"):
                #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.input ] )
                #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.input ] )
                singlefile_galaxyPath$polarity '$singlefile_galaxyPath' singlefile_sampleName$polarity '$singlefile_sampleName'
            #else
                zipfile$polarity '$file_load_section_selected.file_load_conditional.input'
            #end if
        #end if
    </token>

    <token name="@COMMAND_FILE_LOAD_ONE@">
        #set file_load_section_selected = $acquisition_options.file_load_section
        #set polarity=""
        @COMMAND_FILE_LOAD_NEUTRAL@
    </token>

    <token name="@COMMAND_FILE_LOAD_POSITIVE@">
        #set file_load_section_selected = $acquisition_options.file_load_sectionPositive
        #set polarity="Positive"
        @COMMAND_FILE_LOAD_NEUTRAL@
    </token>

    <token name="@COMMAND_FILE_LOAD_NEGATIVE@">
        #set file_load_section_selected = $acquisition_options.file_load_sectionNegative
        #set polarity="Negative"
        @COMMAND_FILE_LOAD_NEUTRAL@
    </token>

    <xml name="input_file_load" token_polarity="">
        <section name="file_load_section@POLARITY@" title="@POLARITY@ Resubmit your raw dataset or your zip file">
            <conditional name="file_load_conditional">
                <param name="file_load_select" type="select" label="@POLARITY@ Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
                    <option value="no" >no need</option>
                    <option value="yes" >yes</option>
                </param>
                <when value="no">
                </when>
                <when value="yes">
                    <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
                </when>
            </conditional>
        </section>
    </xml>

    <xml name="test_commun">
        <section name="getannot">
            <param name="allowMiss" value="TRUE" />
            <conditional name="option_toexclude">
                <param name="option" value="hide" />
            </conditional>
        </section>
        <section name="db">
            <param name="kegg_db" value="KEGG" />
            <param name="ppm_tol" value="8" />
        </section>
        <section name="export">
            <param name="prob" value="count" />
            <param name="html" value="FALSE" />
        </section>
        <section name="reac2cor">
            <param name="opt" value="cor" />
            <param name="corprob" value="0.8" />
            <param name="pcorprob" value="0.8" />
            <param name="corths" value="0.75" />
        </section>
    </xml>

    <xml name="test_file_load_zip">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <param name="input" value="faahKO_reduce.zip" ftype="zip" />
            </conditional>
        </section>
    </xml>

    <xml name="test_file_load_single" token_polarity="">>
        <section name="file_load_section@POLARITY@">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
            </conditional>
        </section>
    </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 (and Gildas Le Corguillé) from 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>