comparison combine.xml @ 9:7e18fcb92a6a draft

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

8:525f201b86c1

<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.1">
    <description>
        combine several mass spectrometry imaging datasets into one
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.2.1">r-ggplot2</requirement>
        <requirement type="package" version="0.12">r-maldiquantforeign</requirement>
        <requirement type="package" version="1.19.3">r-maldiquant</requirement>
    </expand>
    <command detect_errors="exit_code">
    <![CDATA[

            msidata_$i\$column2 = NULL
            msidata_$i\$column3 = NULL
            msidata_$i\$column4 = NULL
            msidata_$i\$column5 = NULL
            msidata_$i\$combined_sample = NULL
        #end if

    ## coercion into MSImageSet
    msidata_$i = as(msidata_$i, "MSImageSet")

    ## remove duplicated coordinates, otherwise combine will fail
    print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file"))
    msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))]

    ## same name for MSI data files necessary to combine data into one single coordinate system
    sampleNames(msidata_$i) = "msidata"

############ 3) Read and process annotation tabular files ######################

    #if str($annotation_cond.annotation_tabular) == 'annotation'
        print("annotations")

   #if not $processed_true:
       ## combine only valid datasets

        valid_data =  list(#echo ','.join($msidata)#)[valid_dataset]
        msidata = do.call(combine, valid_data)
        print("Valid datasets in order of input bottom to top:")
        print(valid_dataset)
        writeImzML(msidata, "out")

    #else

        ## remove duplicated coordinates
        datasetlist = list()
        count = 1
        for (usable_dataset in list(#echo ','.join($msidata)#)){
            pixelsofinterest = pixels(usable_dataset)[names(pixels(usable_dataset)) %in% rownames(coordinates_combined)]
            filtered_dataset = usable_dataset[,pixelsofinterest]
            if (ncol(filtered_dataset) > 0 ){
                datasetlist[[count]] = filtered_dataset}
            count = count +1}

        msidata = do.call(combine, datasetlist)
        writeImzML(msidata, "out")

    #else

        ## in case user made mistake with xy shifts: find duplicated coordinates

    ]]></configfile>
    </configfiles>
    <inputs>
        <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
            label="MSI data"
            help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/>
        <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
        <conditional name="processed_cond">
            <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
                <option value="no_processed" selected="True">no</option>
                <option value="processed">yes</option>

9:7e18fcb92a6a

<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.0">
    <description>
        combine several mass spectrometry imaging datasets into one
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.3.2">r-ggplot2</requirement>
        <requirement type="package" version="0.12">r-maldiquantforeign</requirement>
        <requirement type="package" version="1.19.3">r-maldiquant</requirement>
    </expand>
    <command detect_errors="exit_code">
    <![CDATA[

            msidata_$i\$column2 = NULL
            msidata_$i\$column3 = NULL
            msidata_$i\$column4 = NULL
            msidata_$i\$column5 = NULL
            msidata_$i\$combined_sample = NULL
            msidata_$i <- as(msidata_$i, "MSImagingExperiment")
        #end if

    ## remove duplicated coordinates, otherwise combine will fail
    print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file"))
    msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))]

    ## same name for MSI data files necessary to combine data into one single coordinate system
    run(msidata_$i) = "msidata"

############ 3) Read and process annotation tabular files ######################

    #if str($annotation_cond.annotation_tabular) == 'annotation'
        print("annotations")

   #if not $processed_true:
       ## combine only valid datasets

        valid_data =  list(#echo ','.join($msidata)#)[valid_dataset]
        msidata = do.call(cbind, valid_data)
        print("Valid datasets in order of input bottom to top:")
        print(valid_dataset)
        writeImzML(msidata, "out")

    #else

        ## remove duplicated coordinates
        datasetlist = list()
        count = 1
        for (usable_dataset in list(#echo ','.join($msidata)#)){
        
            pixelsofinterest = paste(coord(usable_dataset)\$x, coord(usable_dataset)\$y, sep="_") %in% paste(coordinates_combined\$x, coordinates_combined\$y, sep="_")           
            filtered_dataset = usable_dataset[,pixelsofinterest]
            if (ncol(filtered_dataset) > 0 ){
                datasetlist[[count]] = filtered_dataset}
            count = count +1}
        msidata = do.call(cbind, datasetlist)
        writeImzML(msidata, "out")

    #else

        ## in case user made mistake with xy shifts: find duplicated coordinates

    ]]></configfile>
    </configfiles>
    <inputs>
        <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
            label="MSI data"
            help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal 'MSImageSet'  or 'MSImagingExperiment' saved as RData (regular upload)"/>
        <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
        <conditional name="processed_cond">
            <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
                <option value="no_processed" selected="True">no</option>
                <option value="processed">yes</option>