comparison macros.xml @ 16:798da6bdff3d draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"

15:accf9fb6ea01

    <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[
        **Input data**

        - 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: 

                           ...
                           ...    

    ]]></token>
    <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
        - Optional file with pixel coordinates and annotation: 

            - Tabular file: One column with x values, one column with y values and one column with annotations
            - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
            - Pixel with coordinates outside the coordinates of the input file are ignored

                ::

                      x_coord     y_coord    annotation
                        1            1        healthy
                        2            1        healthy
                        3            1        disease
                        ...
                        ...

    ]]></token>

    <xml name="reading_msidata">
        <param name="infile" type="data" format="imzml,rdata,analyze75"
               label="MSI data"

16:798da6bdff3d

    <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[
        **Input data**

        - 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/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: 

                           ...
                           ...    

    ]]></token>
    <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
        - Optional file with pixel coordinates and annotation:

            - Tabular file: One column with x values, one column with y values and one column with annotations
            - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
            - Pixel with coordinates outside the coordinates of the input file are ignored


                ::
                
                      x_coord     y_coord    annotation
                        1            1        healthy
                        2            1        healthy
                        3            1        disease
                        ...
                        ...
    ]]></token>

    <xml name="reading_msidata">
        <param name="infile" type="data" format="imzml,rdata,analyze75"
               label="MSI data"