comparison macros_xcms.xml @ 38:67ee46ce9781 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513

37:35a20d7c9f33

    </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>

        #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="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>

    </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

38:67ee46ce9781

    </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 saying 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>

        #if $peaklist.peaklistBool
            convertRTMinute $peaklist.convertRTMinute
            numDigitsMZ $peaklist.numDigitsMZ
            numDigitsRT $peaklist.numDigitsRT
            intval $peaklist.intval
            naTOzero $peaklist.naTOzero
        #end if
    </token>

    <xml name="input_peaklist">
        <conditional name="peaklist">

              <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>
              <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/>
            </when>
            <when value="false" />
        </conditional>
    </xml>

    </token>

    <token name="@HELP_XCMS_MANUAL@">

For details and explanations concerning all the parameters and 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