view macros.xml @ 31:281786a7b9a2 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f

<?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>
            <requirement type="package" version="6.0">unzip</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>

    <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>

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

    <token name="@COMMAND_FILE_LOAD@">
        #if $file_load_section.file_load_conditional.file_load_select == "yes":
            #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
                #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
                #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )

                singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
            #else
                zipfile '$file_load_section.file_load_conditional.input'
            #end if
        #end if
    </token>

    <xml name="input_file_load">
        <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
            <conditional name="file_load_conditional">
                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
                    <option value="no" >no need</option>
                    <option value="yes" >yes</option>
                </param>
                <when value="no">
                </when>
                <when value="yes">
                    <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
                </when>
            </conditional>
        </section>
    </xml>

    <xml name="test_file_load_zip">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <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" />
            </conditional>
        </section>
    </xml>

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

    <xml name="input_peaklist">
        <conditional name="peaklist">
            <param name="peaklistBool" type="boolean" label="Get a Peak List" />
            <when value="true">
              <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
              <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
              <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
              <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
                  <option value="into" selected="true">into</option>
                  <option value="maxo">maxo</option>
                  <option value="intb">intb</option>
              </param>
            </when>
            <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@">
.. 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_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>
        </citations>
    </xml>
</macros>