annotate spectra_plots.xml @ 14:1693b2126f30 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 180894cfabbee2d308be140a0f0b4dba119e88d4-dirty"

<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.3">
    <description>
        mass spectrometry imaging mass spectra plots
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.3.2">r-ggplot2</requirement>
        <requirement type="package" version="2.3">r-gridextra</requirement>
        <requirement type="package" version="1.1.1">r-scales</requirement>
    </expand>
    <command detect_errors="exit_code">
    <![CDATA[
        @INPUT_LINKING@
        cat '${MSI_mzplots}' &&
        Rscript '${MSI_mzplots}'
    ]]>
    </command>
    <configfiles>
        <configfile name="MSI_mzplots"><![CDATA[

################################# load libraries and read file #################

library(Cardinal)
library(gridExtra)
library(ggplot2)
library(scales)


@READING_MSIDATA_FULLY_COMPATIBLE@

@DATA_PROPERTIES@


######################################## PDF ###################################
################################################################################
################################################################################


pdf("mzplots.pdf", fonts = "Times", pointsize = 12)
plot(0,type='n',axes=FALSE,ann=FALSE)
#if not $filename:
    #set $filename = $infile.display_name
#end if
title(main=paste0("Mass spectra for file: \n\n","$filename"))


############################# I) numbers ######################################
###############################################################################

grid.table(property_df, rows= NULL)

## run only if mz and pixels are > 0

if (ncol(msidata)>0 & nrow(msidata) >0){

    pixeldf = data.frame(matrix(ncol = 2, nrow=0))

    ############################# single pixel ################################
    ###########################################################################

    #if str( $pixel_conditional.pixel_type) == 'tabular_pixel':
        print("tabular_pixel")

        ## read and extract x,y, optional annotation information
        spectra_tabular = read.delim("$pixel_conditional.pixel_file", header = $pixel_conditional.tabular_pixel_header, stringsAsFactors = FALSE)

        #if str($pixel_conditional.single_or_overlaid.plot_type) == 'overlaid_plots':

                spectra_input = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y, $pixel_conditional.single_or_overlaid.column_pixel_annotation)]
                colnames(spectra_input) = c("x", "y", "annotation")
                spectra_input\$annotation = as.character(spectra_input\$annotation)
                
                ## keeping only spectra with annotations
                input_pixels = paste(spectra_input[,1], spectra_input[,2], sep="_")
                dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
                pixelsofinterest = dataset_pixels %in% input_pixels
                msidata = msidata[,pixelsofinterest]

                msidata_coordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata)))
                colnames(msidata_coordinates) = c("x", "y", "pixel_index")
                merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"), all.x=TRUE)
                merged_annotation[is.na(merged_annotation)] = "NA"
                merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
                msidata\$annotation = factor(merged_annotation[,4], levels = unique(as.character(merged_annotation[,4]))) ## keep the right order
                
print(msidata\$annotation)
print(merged_annotation)
                 
                    ## overview plot over annotated samples
                    number_combined = length(levels(msidata\$annotation))

                    ## the more annotation groups a file has the smaller will be the legend
                    if (number_combined<20){
                        legend_size = 10
                    }else if (number_combined>20 && number_combined<40){
                        legend_size = 9
                    }else if (number_combined>40 && number_combined<60){
                        legend_size = 8
                    }else if (number_combined>60 && number_combined<100){
                        legend_size = 7
                    }else{
                        legend_size = 6
                    }

                    ## colours selection:

                    #if str($pixel_conditional.single_or_overlaid.colour_conditional.colour_type) == "manual_colour"
                        #set $color_string = ','.join(['"%s"' % $color.annotation_color for $color in $pixel_conditional.single_or_overlaid.colour_conditional.colours])
                        colourvector = c($color_string)

                    #elif str($pixel_conditional.single_or_overlaid.colour_conditional.colour_type) == "colourpalette"

                    	number_levels = (length(levels(msidata\$annotation)))
                    
        	    	colourvector = noquote($pixel_conditional.single_or_overlaid.colour_conditional.palettes)(number_levels)

                    #end if
                    
                    position_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, as.factor(msidata\$annotation))
                    colnames(position_df) = c("x", "y", "sample_name")
print(position_df)
                    combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
                           geom_tile(height = 1, width=1)+
                           coord_fixed()+
                           ggtitle("Spatial orientation of annotations")+
                           theme_bw()+
                           theme(plot.title = element_text(hjust = 0.5))+
                           theme(text=element_text(family="ArialMT", face="bold", size=12))+
                           theme(legend.position="bottom",legend.direction="vertical")+
                           theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 10))+
                           guides(fill=guide_legend(ncol=4,byrow=TRUE))+
                           scale_discrete_manual(aesthetics = c("colour", "fill"), values = colourvector)

                       coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
                       coord_labels\$file_number = 1:nrow(coord_labels)

                    for(file_count in 1:nrow(coord_labels))
                    	{combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
                    	y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))
                    }

                    print(combine_plot)

                    ## print legend only for less than 10 samples
                    if (length(levels(msidata\$annotation)) < 10){
                        key_legend = TRUE
                    }else{key_legend = FALSE}

                #if $fullmz:
                ## plot single tabular mz, average per annotation
                    print(plot(msidata, run="infile", pixel.groups=msidata\$annotation, key=key_legend,superpose=TRUE, strip=FALSE, grid=$grid_variable, col = colourvector), main="Average spectrum per group")
                #end if

                    pixeldf = data.frame(table(msidata\$annotation))
                    colnames(pixeldf) = c("sample name", "number of pixels")

            ##################### II) Sample: plot zoom-in mass spectrum ##########

                #if str($mz_range.mz_range_options) == "manual_mz":

                    #for $token in $mz_range.zoomed_sample:


                minmasspixel = tryCatch(
                        {
                        features(msidata, mz=$token.xlimmin)
                        },
                        warning=function(cond) {
                        ## if xlimmin is outside mz range, use min mz value
                        return(features(msidata, mz=min(mz(msidata))))
                        }
                    )    

                maxmasspixel = tryCatch(
                        {
                        features(msidata, mz=$token.xlimmax)
                        },
                        warning=function(cond) {
                        ## if xlimax is outside mz range, use max mz value
                        return(features(msidata, mz=max(mz(msidata))))
                        }
                    )   

                        ## plot single tabular mz, average per annotation, manual zoom
                        print(plot(msidata[minmasspixel:maxmasspixel,], run="infile", strip=FALSE, col = colourvector,
                        xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation, grid = $grid_variable,
                        key=key_legend, superpose=TRUE, main="Average spectrum per group"))
                    #end for

                #elif str($mz_range.mz_range_options) == "tabular_mz":

                    input_mz = read.delim("$mz_range.mz_file", header = $mz_range.tabular_header, stringsAsFactors = FALSE)
                    input_mz_features = input_mz[,c($mz_range.column_mz)]
                    for (feature_count in input_mz_features){

                        if (feature_count>min(mz(msidata))&feature_count<max(mz(msidata))){

                            xlimmin = feature_count-$mz_range.minus_mz_tab
                            xlimmax = feature_count+$mz_range.plus_mz_tab

                            minmasspixel = features(msidata, mz=xlimmin)
                            maxmasspixel = features(msidata, mz=xlimmax)

                            ## plot single tabular mz, average per annotation, tabular zoom
                            print(plot(msidata[minmasspixel:maxmasspixel,], run="infile", strip=FALSE, main="Average spectrum per group",
                            xlim= c(xlimmin,xlimmax),pixel.groups=msidata\$annotation, grid = $grid_variable, col = colourvector,
                            key=key_legend, superpose=TRUE))

                        }
                    }

                #end if
        #elif str($pixel_conditional.single_or_overlaid.plot_type) == 'separate_plots':


            spectra_tabular = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y)]
            colnames(spectra_tabular) = c("x", "y")

            dataset_pixels = data.frame(coord(msidata)\$x, coord(msidata)\$y)
            colnames(dataset_pixels) = c("x", "y")
            spectra_input = merge(dataset_pixels, spectra_tabular, by=c("x", "y"))
            false_input = merge(spectra_tabular, spectra_input, by=c("x", "y"))

                ## for loop for every valid spectrum (pixel)
                for (pixel_count in 1:nrow(spectra_input)){

                    x_coord = spectra_input[pixel_count,1]
                    y_coord = spectra_input[pixel_count,2]


            ##################### I) Sample: plot full mass spectrum ##############

                    #if $fullmz:
                    ## plot full mz for single tabular mz
                        print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable, col="black"))
                    #end if

                    pixelname = paste0("x = ", x_coord,", ", "y = ", y_coord)

                    input_pixels = paste(x_coord, y_coord, sep="_")
                    dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
                    pixelisvalid = as.character(input_pixels %in% dataset_pixels)

                    pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))


            ##################### II) Sample: plot zoom-in mass spectrum ##########

            #if str($mz_range.mz_range_options) == "manual_mz":
                #for $token in $mz_range.zoomed_sample:

                minmasspixel = tryCatch(
                        {
                        features(msidata, mz=$token.xlimmin)
                        },
                        warning=function(cond) {
                        ## if xlimmin is outside mz range, use min mz value
                        return(features(msidata, mz=min(mz(msidata))))
                        }
                    )    

                maxmasspixel = tryCatch(
                        {
                        features(msidata, mz=$token.xlimmax)
                        },
                        warning=function(cond) {
                        ## if xlimax is outside mz range, use max mz value
                        return(features(msidata, mz=max(mz(msidata))))
                        }
                    )   

                ## same min and max not possible for plot
                if (minmasspixel == maxmasspixel){
                    if (maxmasspixel == nrow(msidata)){
                        minmasspixel = minmasspixel-1
                        }else{
                            maxmasspixel = maxmasspixel+1
                        }
                }

                    ## print single tabular mz; manual zoom

                    tryCatch(
                        {
                        print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black"))
                        }
                        ,
                        error=function(cond) {
                        ## if there are no intensities > 0 in the chosen plotting window, write a warning
                        text(0.5,0.5,labels = c(paste("No peaks in the spectrum with the coordinates x =", x_coord, ", y =", y_coord, sep=" ")))
                        }
                   )

                #end for

                #elif str($mz_range.mz_range_options) == "tabular_mz":

                    input_mz = read.delim("$mz_range.mz_file", header = $mz_range.tabular_header, stringsAsFactors = FALSE)
                    input_mz_features = input_mz[,c($mz_range.column_mz)]
                    for (feature_count in input_mz_features){

                        if (feature_count>min(mz(msidata))&feature_count<max(mz(msidata))){

                            xlimmin = feature_count-$mz_range.minus_mz_tab
                            xlimmax = feature_count+$mz_range.plus_mz_tab

                            minmasspixel = tryCatch(
                                    {
                                    features(msidata, mz=xlimmin)
                                    },
                                    warning=function(cond) {
                                    ## if xlimmin is outside mz range, use min mz value
                                    return(features(msidata, mz=min(mz(msidata))))
                                    }
                                )    

                            maxmasspixel = tryCatch(
                                    {
                                    maxmasspixel = features(msidata, mz=xlimmax)
                                    },
                                    warning=function(cond) {
                                    ## if xlimax is outside mz range, use max mz value
                                    return(features(msidata, mz=max(mz(msidata))))
                                    }
                                )   

                            ## same min and max not possible for plot
                            if (minmasspixel == maxmasspixel){
                                if (maxmasspixel == nrow(msidata)){
                                    minmasspixel = minmasspixel-1
                                    }else{
                                        maxmasspixel = maxmasspixel+1
                                    }
                            }

                                ## print single tabular mz; tabular zoom
                                print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax), col="black"))
                            }
                        }

                #end if

            }

                    colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")

        #end if


    ############################# all pixel ################################
    ###########################################################################

    #elif str( $pixel_conditional.pixel_type) == 'all_pixel':
        print("all pixels")

        ##################### I) Sample: plot full mass spectrum ##############

                    #if $fullmz:

                        print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable, col="black"))
                    #end if

        ##################### II) Sample: plot zoom-in mass spectrum ##########

        #if str($mz_range.mz_range_options) == "manual_mz":
            #for $token in $mz_range.zoomed_sample:

                minmasspixel = tryCatch(
                        {
                        features(msidata, mz=$token.xlimmin)
                        },
                        warning=function(cond) {
                        ## if xlimmin is outside mz range, use min mz value
                        return(features(msidata, mz=min(mz(msidata))))
                        }
                    )    

                maxmasspixel = tryCatch(
                        {
                        features(msidata, mz=$token.xlimmax)
                        },
                        warning=function(cond) {
                        ## if xlimax is outside mz range, use max mz value
                        return(features(msidata, mz=max(mz(msidata))))
                        }
                    )   

                ## same min and max not possible for plot
                if (minmasspixel == maxmasspixel){
                    if (maxmasspixel == nrow(msidata)){
                        minmasspixel = minmasspixel-1
                        }else{
                            maxmasspixel = maxmasspixel+1
                        }
                }

                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black"))

            #end for

        #elif str($mz_range.mz_range_options) == "tabular_mz":

            input_mz = read.delim("$mz_range.mz_file", header = $mz_range.tabular_header, stringsAsFactors = FALSE)
            input_mz_features = input_mz[,c($mz_range.column_mz)]
            for (feature_count in input_mz_features){

                if (feature_count>min(mz(msidata))&feature_count<max(mz(msidata))){

                    xlimmin = feature_count-$mz_range.minus_mz_tab
                    xlimmax = feature_count+$mz_range.plus_mz_tab

                            minmasspixel = tryCatch(
                                    {
                                    features(msidata, mz=xlimmin)
                                    },
                                    warning=function(cond) {
                                    ## if xlimmin is outside mz range, use min mz value
                                    return(features(msidata, mz=min(mz(msidata))))
                                    }
                                )    

                            maxmasspixel = tryCatch(
                                    {
                                    maxmasspixel = features(msidata, mz=xlimmax)
                                    },
                                    warning=function(cond) {
                                    ## if xlimax is outside mz range, use max mz value
                                    return(features(msidata, mz=max(mz(msidata))))
                                    }
                                )   

                        print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax), col="black"))
                }
            }


        #end if

            pixeldf = data.frame("$filename", ncol(msidata))
            colnames(pixeldf) = c("sample name", "number of pixels")

    #end if


############################# pixel table ######################################
###############################################################################


    ### overview table of pixels or samples:
    plot(0,type='n',axes=FALSE,ann=FALSE)
    title(main="Overview of chosen pixel:")

    ### for more than 20 annotation groups print only 20 samples per page:
    if (is.null(levels(msidata\$annotation))){
        grid.table(pixeldf, rows= NULL)
    }else if (length(levels(msidata\$annotation)) <= 20){
        grid.table(pixeldf, rows= NULL)
    }else{
        grid.table(pixeldf[1:20,], rows= NULL)
        mincount = 21
        maxcount = 40
        for (count20 in 1:(ceiling(nrow(pixeldf)/20)-1)){
            plot(0,type='n',axes=FALSE,ann=FALSE)
            if (maxcount <= nrow(pixeldf)){
                grid.table(pixeldf[mincount:maxcount,], rows= NULL)
                mincount = mincount+20
                maxcount = maxcount+20
            }else{### stop last page with last sample otherwise NA in table
                grid.table(pixeldf[mincount:nrow(pixeldf),], rows= NULL)} 
        }
    }

    dev.off()

}else{
    print("Inputfile has no intensities > 0")
    dev.off()
}


    ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="reading_msidata"/>
        <expand macro="pdf_filename"/>
        <conditional name="pixel_conditional">
            <param name="pixel_type" type="select" label="Choose spectra">
                <option value="all_pixel" selected="True" >Plot mean spectra based on all spectra</option>
                <option value="tabular_pixel">Plot single spectra (separate or overlaid)</option>
            </param>
            <when value="tabular_pixel">
                <param name="pixel_file" type="data" format="tabular" label="Load tabular file with pixel coordinates"
                help="Two or three columns: x values, y values, optionally annotations"/>
                <param name="column_pixel_x" data_ref="pixel_file" label="Column with x values" type="data_column"/>
                <param name="column_pixel_y" data_ref="pixel_file" label="Column with y values" type="data_column"/>
                <param name="tabular_pixel_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
                <conditional name="single_or_overlaid">
		    <param name="plot_type" type="select" label="Separate plot per spectrum or overlaid plot with average spectra per annotation group">
		        <option value="separate_plots" selected="True" >Separate spectra plots</option>
		        <option value="overlaid_plots">Overlaid spectra plots</option>
		    </param>
		    <when value="separate_plots"/>
		    <when value="overlaid_plots">
		    <param name="column_pixel_annotation" data_ref="pixel_file" label="Select column with annotations" type="data_column"/>
		    <conditional name="colour_conditional">
		        <param name="colour_type" type="select" label="Choose a colour scheme">
			    <option value="colourpalette" selected="True" >Colour palette</option>
			    <option value="manual_colour">Manual selection</option>
			</param>
			<when value="manual_colour">
			   <repeat name="colours" title="Colours for the plots" min="1" max="50">
			   <param name="annotation_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of components">
			   <sanitizer>
			       <valid initial="string.letters,string.digits">
			       <add value="#" />
			       </valid>
			   </sanitizer>
			   </param>
			   </repeat>
			</when>
			<when value="colourpalette">
			    <param name="palettes" type="select" display="radio" label="Select a colourpalette">
			        <option value="hue_pal()" selected="True">hue</option>
			        <option value="rainbow">rainbow</option>
				<option value="heat.colors">heat colors</option>
				<option value="terrain.colors">terrain colors</option>
				<option value="topo.colors">topo colors</option>
				<option value="cm.colors">cm colors</option>
			    </param>
			</when>
		    </conditional>
                    </when>
                </conditional>
            </when>
            <when value="all_pixel">
            </when>
        </conditional>
        <param name="fullmz" type="boolean" label="Plot complete m/z range" checked="True" truevalue="TRUE" falsevalue="FALSE"/>
        <conditional name="mz_range">
            <param name="mz_range_options" type="select" label="zoomed in m/z range">
                <option value="none_mz" selected="True">no m/z range</option>
                <option value="manual_mz" >Manual input</option>
                <option value="tabular_mz">Tabular file</option>
            </param>
            <when value="none_mz"/>
            <when value="tabular_mz">
                <param name="minus_mz_tab" type="float" value="" label="m/z value to subtract from m/z values in tabular file = lower m/z boundary"/>
                <param name="plus_mz_tab" type="float" value="" label="m/z value to add to m/z values in tabular file = upper m/z boundary"/>
                <param name="mz_file" type="data" format="tabular" label="Load tabular file with m/z values"/>
                <param name="column_mz" data_ref="mz_file" label="Column with mz values" type="data_column"/>
                <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
            </when>
            <when value="manual_mz">
                <repeat name="zoomed_sample" title="Define min m/z and max m/z for the plotting window" min="1">
                    <param name="xlimmin" type="float" value="" label="lower m/z boundary for plotting window"/>
                    <param name="xlimmax" type="float" value="" label="upper m/z boundary for plotting window"/>
                </repeat>
            </when>
        </conditional>
        <param name="grid_variable" type="boolean" label="Add grid to plot" truevalue="TRUE" falsevalue="FALSE"/>
    </inputs>
    <outputs>
        <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label="${tool.name} on ${on_string}:results"/>
    </outputs>
    <tests>
        <test>
            <expand macro="infile_imzml"/>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="tabular_pixel"/>
                <param name="pixel_file" value="spectra_1_pixel.tabular"/>
                <param name="column_pixel_x" value="1"/>
                <param name="column_pixel_y" value="2"/>
                <param name="tabular_pixel_header" value="FALSE"/>
            </conditional>
                <param name="fullmz" value="TRUE"/>
                <conditional name="mz_range">
                    <param name="mz_range_options" value="manual_mz"/>
                    <repeat name="zoomed_sample">
                        <param name="xlimmin" value="310"/>
                        <param name="xlimmax" value="320"/>
                    </repeat>
                   <repeat name="zoomed_sample">
                        <param name="xlimmin" value="350"/>
                        <param name="xlimmax" value="400"/>
                    </repeat>
                   <repeat name="zoomed_sample">
                        <param name="xlimmin" value="360"/>
                        <param name="xlimmax" value="360.8"/>
                    </repeat>
                </conditional>
                <param name="grid_variable" value="TRUE"/>
            <output name="plots" file="Plot_imzml.pdf" compare="sim_size"/>
        </test>
        <test>
            <expand macro="infile_analyze75"/>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="tabular_pixel"/>
                <param name="pixel_file" value="spectra_1_pixel.tabular"/>
                <param name="column_pixel_x" value="1"/>
                <param name="column_pixel_y" value="2"/>
                <param name="tabular_pixel_header" value="TRUE"/>
            </conditional>
                <param name="fullmz" value="TRUE"/>
                <conditional name="mz_range">
                    <param name="mz_range_options" value="manual_mz"/>
                    <repeat name="zoomed_sample">
                        <param name="xlimmin" value="840"/>
                        <param name="xlimmax" value="850"/>
                    </repeat>
                </conditional>
                <param name="grid_variable" value="FALSE"/>
            <output name="plots" file="Plot_analyze75.pdf" compare="sim_size"/>
        </test>
        <test>
            <expand macro="infile_analyze75"/>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="tabular_pixel"/>
                <param name="pixel_file" value="annotations.tabular"/>
                <param name="column_pixel_x" value="1"/>
                <param name="column_pixel_y" value="2"/>
                <param name="tabular_pixel_header" value="TRUE"/>

                <conditional name="single_or_overlaid">
                    <param name="plot_type" value="overlaid_plots"/>
                    <param name="column_pixel_annotation" value="4"/>
                    <param name="colour_type" value="manual_colour"/>
                    <repeat name="colours">
                        <param name="annotation_color" value="#0000FF"/>
		    </repeat>
		    <repeat name="colours">
			<param name="annotation_color" value="#00C957"/>
		    </repeat>
		    <repeat name="colours">
			<param name="annotation_color" value="#B0171F"/>
		    </repeat>
                </conditional>
            </conditional>
		<param name="fullmz" value="FALSE"/>
		<conditional name="mz_range">
		    <param name="mz_range_options" value="manual_mz"/>
		    <repeat name="zoomed_sample">
		        <param name="xlimmin" value="1250"/>
		        <param name="xlimmax" value="1270"/>
		    </repeat>
		</conditional>
		<param name="grid_variable" value="FALSE"/>
	    <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size"/>
        </test>
        <test>
            <param name="infile" value="3_files_combined.RData" ftype="rdata"/>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="all_pixel"/>
            </conditional>
                <param name="fullmz" value="TRUE"/>
                <conditional name="mz_range">
                    <param name="mz_range_options" value="manual_mz"/>
                    <repeat name="zoomed_sample">
                        <param name="xlimmin" value="350"/>
                        <param name="xlimmax" value="360"/>
                    </repeat>
                </conditional>
                <param name="grid_variable" value="FALSE"/>
            <output name="plots" file="Plot_rdata.pdf" compare="sim_size"/>
        </test>
        <test>
            <expand macro="processed_infile_imzml"/>
            <conditional name="processed_cond">
                <param name="processed_file" value="processed"/>
                <param name="accuracy" value="100"/>
                <param name="units" value="ppm"/>
            </conditional>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="all_pixel"/>
            </conditional>
                <param name="fullmz" value="FALSE"/>
                <conditional name="mz_range">
                    <param name="mz_range_options" value="manual_mz"/>
                    <repeat name="zoomed_sample">
                        <param name="xlimmin" value="350"/>
                        <param name="xlimmax" value="350.5"/>
                    </repeat>
                    <repeat name="zoomed_sample">
                        <param name="xlimmin" value="600"/>
                        <param name="xlimmax" value="650"/>
                    </repeat>
                </conditional>
                <param name="grid_variable" value="TRUE"/>
            <output name="plots" file="Plot_processed.pdf" compare="sim_size"/>
        </test>
        <test>
        <param name="infile" value="" ftype="imzml">
            <composite_data value="preprocessing_results1.imzml"/>
            <composite_data value="preprocessing_results1.ibd"/>
        </param>
        <param name="centroids" value="TRUE"/>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="all_pixel"/>
            </conditional>
                <param name="fullmz" value="TRUE"/>
                <conditional name="mz_range">
                    <param name="mz_range_options" value="manual_mz"/>
                    <repeat name="zoomed_sample">
                        <param name="xlimmin" value="328"/>
                        <param name="xlimmax" value="330"/>
                    </repeat>
                    <repeat name="zoomed_sample">
                        <param name="xlimmin" value="335"/>
                        <param name="xlimmax" value="340"/>
                    </repeat>
                </conditional>
            <param name="grid_variable" value="TRUE"/>
            <output name="plots" file="Plot_picked.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

@CARDINAL_DESCRIPTION@

-----

This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass spectrometry imaging data.

@MSIDATA_INPUT_DESCRIPTION@

@SPECTRA_TABULAR_INPUT_DESCRIPTION@

@MZ_TABULAR_INPUT_DESCRIPTION@

**Options**

*Choosing spectra*

- "All spectra": Plots average mass spectra (mean of all spectra)

- "Single spectra": Returns a full mass spectrum plot for each input spectrum, which is defined by its x- and y-coordinates

    - the annotation column is optional: 
    - without annotation column: plots a separate mass spectrum for every input spectrum
    - with annotation column: plots average mass spectra for each annotation group in different colours


*Choosing m/z axis*

- "Plot complete m/z range": Full m/z range is plotted

- "zoomed in m/z range": Only a customized m/z range is plotted


    - "Manual input": Provide the minimum and maximum m/z value to define the m/z axis of the plot

    - "Tabular input": File with m/z values of interest. Needs manual choice of m/z values to subtract and add from the input m/z values to generate the m/z axis of the plot


**Output**

- Single Pdf with all mass spectra plots


]]>
    </help>
    <expand macro="citations"/>
</tool>