annotate macros.xml @ 8:d1ce2634135f draft

planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 88163f9ba0e3e95f00e18247c67b95cf7791fa98-dirty

<?xml version="1.0"?>

<macros>

    <token name="@TOOL_VERSION@">1.22.1</token>

	<xml name="stdio">
        <stdio>
            <exit_code range="1" level="fatal" />
        </stdio>
	</xml>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bioconductor-metams</requirement>
            <requirement type="package" version="1.1_5">r-batch</requirement>
            <yield />
        </requirements>
    </xml>

	<xml name="input_file_load">
        <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
            <conditional name="file_load_conditional">
                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message saying 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_file_load_alg">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <param name="input" value="RawFilesTest_alg2_t.mzData,RawFilesTest_alg3_t.mzData,RawFilesTest_alg7_t.mzData,RawFilesTest_alg8_t.mzData,RawFilesTest_alg9_t.mzData,RawFilesTest_alg11_t.mzData" ftype="mzdata" />
            </conditional>
        </section>
	</xml>-->

	<xml name="test_file_load_alg_symlink">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <param name="input" value="alg2.mzData,alg3.mzData,alg7.mzData,alg8.mzData,alg9.mzData,alg11.mzData" ftype="mzdata" />
            </conditional>
        </section>
	</xml>

    <!-- COMMAND -->
    <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>

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

    <!-- FILE_LOAD for planemo test -->
    <!-- Change | for , because I use it in metaMS tool -->
    <token name="@COMMAND_FILE_LOAD@">
        #if $file_load_section.file_load_conditional.file_load_select == "yes":
            #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
                #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
                #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )

                singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
            #else
                zipfile '$file_load_section.file_load_conditional.input'
            #end if
        #end if
	</token>

    <token name="@HELP_AUTHORS@">
        .. class:: infomark

        **Author(s)**  Ron Wehrens ([e-mail]), Georg Weingart, Fulvio Mattivi

        .. class:: infomark

        **Galaxy wrapper and scripts developpers** Guitton Yann LABERCA [e-mail] and Saint-Vanne Julien [e-mail]

        .. class:: infomark

        **Please cites**  
 
            metaMS : Wehrens, R.; Weingart, G.; Mattivi, F. Journal of Chromatography B.

            xcms :   Smith, C. A.; Want, E. J.; O’Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779–787.

            CAMERA :   Kuhl, C.; Tautenhahn, R.; Böttcher, C.; Larson, T. R.; Neumann, S. Analytical Chemistry 2012, 84, 283–289.
    </token>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1016/j.jchromb.2014.02.051</citation>
            <citation type="doi">10.1093/bioinformatics/btu813</citation>
        </citations>
    </xml>
    
</macros>