comparison macros.xml @ 9:c3d2ca5f9dd0 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"

8:f3a77d4c4991

<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">

    ]]></token>

    <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ 
########################### QC numbers ########################
## including intensity calculations which need data in RAM
        ## Number of features (mz)
        maxfeatures = length(features(msidata))
        ## Range mz
        minmz = round(min(mz(msidata)), digits=2)
        maxmz = round(max(mz(msidata)), digits=2)

        maximumx = max(coord(msidata)[,1])
        ## Range y coordinates
        minimumy = min(coord(msidata)[,2])
        maximumy = max(coord(msidata)[,2])
        ## Range of intensities
        minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2)
        maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2)
        ## Number of intensities > 0, for if conditions
        npeaks= sum(as.matrix(spectra(msidata))>0, na.rm=TRUE)
        ## Number of NA in spectra matrix
        NAcount = sum(is.na(spectra(msidata)))
        ## Number of NA in spectra matrix
        infcount = sum(is.infinite(as.matrix(spectra(msidata))))
        ## Number of duplicated coordinates
        dupl_coord = sum(duplicated(coord(msidata)))
        properties = c("Number of m/z features",
                       "Range of m/z values",
                       "Number of pixels", 

        - 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:c3d2ca5f9dd0

<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">

    ]]></token>

    <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ 
########################### QC numbers ########################
## including intensity calculations which need data in RAM

	int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use
	## Number of NA in spectra matrix
        NAcount = sum(is.na(int_matrix))
	## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata
	int_matrix[is.na(int_matrix)] <- 0
	
        ## Number of features (mz)
        maxfeatures = length(features(msidata))
        ## Range mz
        minmz = round(min(mz(msidata)), digits=2)
        maxmz = round(max(mz(msidata)), digits=2)

        maximumx = max(coord(msidata)[,1])
        ## Range y coordinates
        minimumy = min(coord(msidata)[,2])
        maximumy = max(coord(msidata)[,2])
        ## Range of intensities
        minint = round(min(int_matrix), digits=2)
        maxint = round(max(int_matrix), digits=2)
        ## Number of intensities > 0, for if conditions
        npeaks= sum(int_matrix>0)
        ## Number of NA in spectra matrix
        infcount = sum(is.infinite(int_matrix))
        ## Number of duplicated coordinates
        dupl_coord = sum(duplicated(coord(msidata)))
        properties = c("Number of m/z features",
                       "Range of m/z values",
                       "Number of pixels", 

        - 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>