comparison macros.xml @ 30:4d6f4cd7c3ef draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e

29:c013ed353a2f

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.4_1">r-snow</requirement>
            <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
            <requirement type="package" version="1.1_4">r-batch</requirement>
        </requirements>
    </xml>
    <xml name="requirements_light">
        <requirements>
            <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1" level="fatal" />
        </stdio>
    </xml>

    <token name="@COMMAND_XCMS_SCRIPT@">
        LC_ALL=C Rscript $__tool_directory__/xcms.r
    </token>

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

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

                <param name="input" value="faahKO_reduce.zip" ftype="zip" />
            </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" />

        </section>
    </xml>

    <token name="@COMMAND_PEAKLIST@">
        #if $peaklist.peaklistBool
            variableMetadataOutput '$variableMetadata'
            dataMatrixOutput '$dataMatrix'
            convertRTMinute $peaklist.convertRTMinute
            numDigitsMZ $peaklist.numDigitsMZ
            numDigitsRT $peaklist.numDigitsRT
            intval $peaklist.intval
        #end if

            <when value="false" />
        </conditional>
    </xml>

    <xml name="output_peaklist"  token_function="">
        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv">
            <filter>(peaklist['peaklistBool'])</filter>
        </data>
        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" >
            <filter>(peaklist['peaklistBool'])</filter>
        </data>
    </xml>

    <token name="@HELP_AUTHORS@">

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

    </token>


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

30:4d6f4cd7c3ef

<?xml version="1.0"?>
<macros>
    <token name="@WRAPPER_VERSION@">3.0.0</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>
            <yield />
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1" level="fatal" />
        </stdio>
    </xml>

    <token name="@COMMAND_XCMS_SCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>

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

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

                <param name="input" value="faahKO_reduce.zip" ftype="zip" />
            </conditional>
        </section>
    </xml>

    <xml name="test_file_load_zip_sacuri">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
            </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" />

        </section>
    </xml>

    <token name="@COMMAND_PEAKLIST@">
        #if $peaklist.peaklistBool
            convertRTMinute $peaklist.convertRTMinute
            numDigitsMZ $peaklist.numDigitsMZ
            numDigitsRT $peaklist.numDigitsRT
            intval $peaklist.intval
        #end if

            <when value="false" />
        </conditional>
    </xml>

    <xml name="output_peaklist"  token_function="">
        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" >
            <filter>(peaklist['peaklistBool'])</filter>
        </data>
        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" >
            <filter>(peaklist['peaklistBool'])</filter>
        </data>
    </xml>

    <token name="@HELP_AUTHORS@">

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

    </token>

    <token name="@HELP_XCMS_MANUAL@">

For details and explanations for all the parameters and the workflow of xcms_ package, see its manual_ and this example_

.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
.. _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_PEAKLIST@">

Get a Peak List
---------------

If 'true', the module generates two additional files corresponding to the peak list:
- the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
- the data matrix (corresponding to related intensities)

**decimal places for [mass or retention time] values in identifiers**

    | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
    | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
    | Theses parameters do not affect decimal places in columns other than the identifier one.

**Reported intensity values**

    | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
    | - into: integrated area of original (raw) peak
    | - maxo: maximum intensity of original (raw) peak
    | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)

    </token>

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