annotate macros.xml @ 10:8828cba9aedd draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857

<?xml version="1.0"?>
<macros>
    <xml name="stdio">
        <stdio>
            <exit_code range="1" level="fatal" />
        </stdio>
    </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>

    <!-- INPUT_VALIDATORS -->
    <xml name="input_validator_range_integer">
        <validator type="regex" message="The format is 'min,max'" >[0-9]+ *, *[0-9]+</validator>
    </xml>

    <xml name="input_validator_range_float">
        <validator type="regex" message="The format is 'min,max'" >[0-9]+\.?[0-9]* *, *[0-9]+\.?[0-9]*</validator>
    </xml>

    <xml name="input_validator_list_integer">
        <validator type="regex" message="The format is '1,2,4,6'" >[0-9, ]+</validator>
    </xml>


    <token name="@INPUT_IMAGE_LABEL@">RData file</token>
    <token name="@INPUT_IMAGE_HELP@">It contains a xcms3::XCMSnExp object (named xdata)</token>


    <!-- MISC -->
    <token name="@HELP_AUTHORS_WRAPPERS@">

.. class:: infomark

**Galaxy integration** ABiMS TEAM - SU/CNRS - Station biologique de Roscoff and Yann Guitton - LABERCA
Part of Workflow4Metabolomics.org [W4M]

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

    </token>

    <xml name="citation_w4m">
            <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </xml>
</macros>