comparison macros.xml @ 29:c013ed353a2f draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298

28:13885e67b123

    <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@">
        LANG=C Rscript $__tool_directory__/xcms.r
    </token>

    <token name="@COMMAND_LOG_EXIT@">
        ;
        return=\$?;

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

    <xml name="input_tic_bpc_pdf">
        <param name="tic_bpc_pdf" type="boolean" checked="False" label="Do you want TIC and BCP in PDF Format" help="Whatever, you will be able to use MultiQC tools on the tabular files" />
    </xml>

    <xml name="test_retcor_param">
        <param name="methods|method" value="peakgroups"/>
        <param name="methods|smooth" value="loess"/>
        <param name="methods|extra" value="1"/>
        <param name="methods|missing" value="1"/>
        <param name="methods|options|option" value="show"/>
        <param name="methods|options|span" value="0.2"/>
        <param name="methods|options|family" value="gaussian"/>
        <param name="methods|options|plottype" value="deviation"/>
    </xml>

    <xml name="test_retcor_output" token_raworcorrected="">
        <output name="log">
            <assert_contents>
                <has_text text="object with 4 samples" />
                <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
                <has_text text="Mass range: 200.1-600 m/z" />
                <has_text text="Peaks: 9251 (about 2313 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: KO, WT" />
            </assert_contents>
        </output>
        <output_collection name="ticsCorrectedTabCollection" type="list">
            <element name="ko15" value="ko15-TIC@RAWORCORRECTED@_mqc.out" />
            <element name="ko16" value="ko16-TIC@RAWORCORRECTED@_mqc.out" />
            <element name="wt15" value="wt15-TIC@RAWORCORRECTED@_mqc.out" />
            <element name="wt16" value="wt16-TIC@RAWORCORRECTED@_mqc.out" />
        </output_collection>
        <output_collection name="bpcsCorrectedTabCollection" type="list">
            <element name="ko15" value="ko15-BPC@RAWORCORRECTED@_mqc.out" />
            <element name="ko16" value="ko16-BPC@RAWORCORRECTED@_mqc.out" />
            <element name="wt15" value="wt15-BPC@RAWORCORRECTED@_mqc.out" />
            <element name="wt16" value="wt16-BPC@RAWORCORRECTED@_mqc.out" />
        </output_collection>
    </xml>

    <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>

    <token name="@HELP_BCP_TIC@">

BPCs and TICs: tabular

    | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs
    | Import BPC and TIC from xcmsSet and retcor [at once] within MultiQC_ (in or outside Galaxy) to display and navigate in the graphs.
    | - In MultiQC: as tool, use the Custom Content

.. _MultiQC: http://multiqc.info/

BPCs and TICs: pdf [if using zip]

    | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs in pdf format.

    </token>

    <token name="@HELP_GET_PEAK_LIST@">

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>

    <token name="@HELP_GET_PEAK_LIST_OUTPUTS@">

xset.variableMetadata.tsv : tabular format [If Get a Peak List == Yes]

    | Table containing information about ions - Can be used in **Normalisation/Generic_filter** and **Statitics** tools.

xset.dataMatrix.tsv : tabular format

    | Table containing ions' intensities - Can be used **Normalisation/Generic_filter** and **Statitics** tools.

    </token>

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

29:c013ed353a2f

    <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=\$?;

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

    <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>