<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.10.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bioconductor-ipo</requirement>
            <requirement type="package" version="1.1_5">r-batch</requirement>
        </requirements>
    </xml>

    <token name="@COMMAND_NSLAVES@"><![CDATA[
        nSlaves \${GALAXY_SLOTS:-1}
    ]]></token>

    <!-- zipfile load for planemo test -->

    <token name="@ESCAPE_IDENTIFIER@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($single_file.element_identifier))]]></token>
    <token name="@COMMAND_FILE_LOAD@"><![CDATA[
        #import re
        #if $file_load_section.file_load_conditional.file_load_select == "yes":
            #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
            #set singlefile_sampleName = '|'.join( ["%s" % re.sub('[^\s\w\-\.]', '_', str($single_file.element_identifier)) for single_file in $file_load_section.file_load_conditional.input ] )

            singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
        #end if
    ]]></token>

    <xml name="input_validator_range_integer">
      <validator type="regex" message="Should be this format: XX or XX,YY">[0-9]+,?[0-9]*</validator>
    </xml>

    <xml name="input_validator_range_float">
        <validator type="regex" message="Should be one combinaison of those format: XX, XX.YY, XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,?[0-9]*[\.]?[0-9]*</validator>
    </xml>

    <xml name="input_validator_range_float_neg">
        <validator type="regex" message="Should be one combinaison of those format: XX, XX.YY, XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,?[\-]?[0-9]*[\.]?[0-9]*</validator>
    </xml>

    <xml name="input_file_load">
        <section name="file_load_section" title="Resubmit your raw dataset">
            <conditional name="file_load_conditional">
                <param name="file_load_select" type="select" label="Resubmit your dataset" help="Use only if you get a message which say that your original dataset 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" 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_file_load_single">
        <section name="file_load_section">
            <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@"><![CDATA[
.. class:: infomark

**Authors**  Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes

.. class:: infomark

**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]

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

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

    ]]></token>
    <token name="@HELP_NEWVERSION_1_10_0_0@"><![CDATA[
**Version 1.10.0+galaxy0 - 03/09/2019**

- NEW: new versions of the IPO wrappers based on IPO-1.10.0
    ]]></token>


    <xml name="citation">
        <citations>
            <citation type="doi">10.1186/s12859-015-0562-8</citation>
            <citation type="doi">10.1093/bioinformatics/btu813</citation>
        </citations>
    </xml>
</macros>