comparison macros_xcms.xml @ 11:37d31fd64eb4 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"

10:dbd877060ac3

              <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"/>
    </xml>

    <xml name="input_peaklist_section">
        <section name="peaklist" title="Peak List" expanded="True">
            <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" />

        </param>
        <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" >
            <option value="wMean">intensity weighted mean of the peak's m/z values</option>
            <option value="mean">mean of the peak's m/z values</option>
            <option value="apex">use the m/z value at the peak apex</option>
            <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
            <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>
        </param>
        <param argument="integrate" type="select" label="Integration method" >
            <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option>
            <option value="2">peak limits based on real data (more accurate but prone to noise)</option>

11:37d31fd64eb4

              <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="If NA values remain, replace them by 0 in the dataMatrix" help="Mandatory for some of the downstream tools (data processing, statistics) that do not accept NA values"/>
    </xml>

    <xml name="input_peaklist_section">
        <section name="peaklist" title="Peak List" expanded="True">
            <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" />

        </param>
        <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" >
            <option value="wMean">intensity weighted mean of the peak's m/z values</option>
            <option value="mean">mean of the peak's m/z values</option>
            <option value="apex">use the m/z value at the peak apex</option>
            <option value="wMeanApex3">intensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
            <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>
        </param>
        <param argument="integrate" type="select" label="Integration method" >
            <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option>
            <option value="2">peak limits based on real data (more accurate but prone to noise)</option>