annotate macros.xml @ 2:54cc3edfe35c draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.1.2">R</requirement>
	    <requirement type="package" version="0.4_1">r-snow</requirement>
            <requirement type="package" version="1.44.0">bioconductor-xcms</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_XCMS_SCRIPT@">
        LANG=C Rscript $__tool_directory__/xcms.r
    </token>

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

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

**Authors**  Colin A. Smith [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann [e-mail], Paul Benton [e-mail] and Christopher Conley [e-mail] 

.. class:: infomark

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

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

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

    </token>


    <xml name="citation">
        <citations>
            <citation type="doi">10.1021/ac051437y</citation>
            <citation type="doi">10.1093/bioinformatics/btu813</citation>
        </citations>
    </xml>
</macros>