comparison macros.xml @ 9:08ebd8da780c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"

8:a69865da6f80

<macros>
    <token name="@VERSION@">2.4.0</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
            <requirement type="package" version="3.6.1">r-base</requirement>
            <yield/>
        </requirements>
    </xml>

    <xml name="print_version">

        - MSI data: 3 types of input data can be used:

            - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
            - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
            - Cardinal "MSImageSet" data saved as .RData
    ]]></token>
    <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
        - Optional tabular file with m/z values: 

            - One column with numeric m/z values (without empty fields or letters)

                <option value="no_processed" selected="True">no</option>
                <option value="processed">yes</option>
            </param>
            <when value="no_processed"/>
            <when value="processed">
                <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
                <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
                    <option value="mz" >mz</option>
                    <option value="ppm" selected="True" >ppm</option>
                </param>
            </when>

9:08ebd8da780c

<macros>
    <token name="@VERSION@">2.6.0</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
            <!--requirement type="package" version="3.6.1">r-base</requirement-->
            <yield/>
        </requirements>
    </xml>

    <xml name="print_version">

        - MSI data: 3 types of input data can be used:

            - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
            - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
            - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData
    ]]></token>
    <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
        - Optional tabular file with m/z values: 

            - One column with numeric m/z values (without empty fields or letters)

                <option value="no_processed" selected="True">no</option>
                <option value="processed">yes</option>
            </param>
            <when value="no_processed"/>
            <when value="processed">
                <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned"/>
                <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
                    <option value="mz" >mz</option>
                    <option value="ppm" selected="True" >ppm</option>
                </param>
            </when>