comparison macros_xcms.xml @ 14:5bd125a3f3b0 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"

13:39797c768bba

<?xml version="1.0"?>
<macros>

    <token name="@TOOL_VERSION@">3.6.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
            <requirement type="package" version="1.1_5">r-batch</requirement>
            <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>

              <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>

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

    </token>

    <token name="@HELP_XCMS_NEWVERSION_3440@">
**Version 3.4.4.0 - 08/02/2019**

    </token>
    <token name="@HELP_XCMS_NEWVERSION_3610@">
**Version 3.6.1+galaxy* - 03/09/2019**

- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
    </token>

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

14:5bd125a3f3b0

<?xml version="1.0"?>
<macros>

    <token name="@TOOL_VERSION@">3.12.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
            <requirement type="package" version="1.1_5">r-batch</requirement>
            <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>

              <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>

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
.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS

    </token>

    <token name="@HELP_XCMS_NEWVERSION_3440@">
**Version 3.4.4.0 - 08/02/2019**

    </token>
    <token name="@HELP_XCMS_NEWVERSION_3610@">
**Version 3.6.1+galaxy* - 03/09/2019**

- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
    </token>
    <token name="@HELP_XCMS_NEWVERSION_31200@">
**Version 3.12.0+galaxy* - 03/03/2020**

- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_)
    </token>

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