comparison macros_xcms.xml @ 13:39797c768bba draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"

12:a301f001835c

<?xml version="1.0"?>
<macros>

    <token name="@WRAPPER_VERSION@">3.4.4</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement>
            <requirement type="package" version="1.1_4">r-batch</requirement>
            <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
            <requirement type="package" version="6.0">unzip</requirement>
            <yield />
        </requirements>
    </xml>

                <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
            </conditional>
        </section>
    </xml>

    <xml name="test_file_load_single_ko15">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <param name="input" value="ko15.CDF" ftype="netcdf" />
            </conditional>
        </section>
    </xml>

    <!-- PEAKLIST -->

            noise $methods.CentWaveAdv.noise
            verboseColumns $methods.CentWaveAdv.verboseColumns
    </token>

    <xml name="input_centwave">
        <param argument="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." />
        <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space.">
            <expand macro="input_validator_range_float"/>
        </param>
    </xml>

.. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
.. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html

    </token>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1021/ac051437y</citation>
            <expand macro="citation_w4m"/>
        </citations>

13:39797c768bba

<?xml version="1.0"?>
<macros>

    <token name="@TOOL_VERSION@">3.6.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
            <requirement type="package" version="1.1_5">r-batch</requirement>
            <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
            <requirement type="package" version="6.0">unzip</requirement>
            <yield />
        </requirements>
    </xml>

                <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
            </conditional>
        </section>
    </xml>

    <xml name="test_file_load_single_file" token_filename="">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <param name="input" value="@FILENAME@.CDF" ftype="netcdf" />
            </conditional>
        </section>
    </xml>

    <!-- PEAKLIST -->

            noise $methods.CentWaveAdv.noise
            verboseColumns $methods.CentWaveAdv.verboseColumns
    </token>

    <xml name="input_centwave">
        <param argument="ppm" type="float" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." />
        <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space.">
            <expand macro="input_validator_range_float"/>
        </param>
    </xml>

.. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
.. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html

    </token>

    <token name="@HELP_XCMS_NEWVERSION_3440@">
**Version 3.4.4.0 - 08/02/2019**

- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
    </token>
    <token name="@HELP_XCMS_NEWVERSION_3610@">
**Version 3.6.1+galaxy* - 03/09/2019**

- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
    </token>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1021/ac051437y</citation>
            <expand macro="citation_w4m"/>
        </citations>