comparison macros.xml @ 18:d9e7403f16f3 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b3ba169290fd2e40dafe167f345106c1c3da3ebe

17:a2908411620e

                </conditional>
            </when>
        </conditional>
    </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]

18:d9e7403f16f3

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