Mercurial > repos > galaxyp > cardinal_spectra_plots
changeset 0:de334e98f1c1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,236 @@ +<macros> + <token name="@VERSION@">1.12.1</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> + <yield/> + </requirements> + </xml> + + <token name="@INPUT_LINKING@"><![CDATA[ + #if $infile.ext == 'imzml' + ln -s '${infile.extra_files_path}/imzml' infile.imzML && + ln -s '${infile.extra_files_path}/ibd' infile.ibd && + #elif $infile.ext == 'analyze75' + ln -s '${infile.extra_files_path}/hdr' infile.hdr && + ln -s '${infile.extra_files_path}/img' infile.img && + ln -s '${infile.extra_files_path}/t2m' infile.t2m && + #else + ln -s $infile infile.RData && + #end if + ]]></token> + + + <token name="@READING_MSIDATA@"><![CDATA[ + ## importing MSI data files + + ## function to read RData files independent of filename + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } + + #if $infile.ext == 'imzml' + #if str($processed_cond.processed_file) == "processed": + msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") + centroided(msidata) = $centroids + #else + msidata <- readImzML('infile') + centroided(msidata) = $centroids + #end if + #elif $infile.ext == 'analyze75' + msidata = readAnalyze('infile') + centroided(msidata) = $centroids + #else + msidata = loadRData('infile.RData') + #end if + + ]]></token> + + <token name="@DATA_PROPERTIES@"><![CDATA[ + ## Number of features (mz) + maxfeatures = length(features(msidata)) + ## Range mz + minmz = round(min(mz(msidata)), digits=2) + maxmz = round(max(mz(msidata)), digits=2) + ## Number of spectra (pixels) + pixelcount = length(pixels(msidata)) + ## Range x coordinates + minimumx = min(coord(msidata)[,1]) + maximumx = max(coord(msidata)[,1]) + ## Range y coordinates + minimumy = min(coord(msidata)[,2]) + maximumy = max(coord(msidata)[,2]) + ## Range of intensities + minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2) + maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2) + ## Number of intensities > 0, for if conditions + npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE) + + properties = c("Number of m/z features", + "Range of m/z values", + "Number of pixels", + "Range of x coordinates", + "Range of y coordinates", + "Range of intensities") + + values = c(paste0(maxfeatures), + paste0(minmz, " - ", maxmz), + paste0(pixelcount), + paste0(minimumx, " - ", maximumx), + paste0(minimumy, " - ", maximumy), + paste0(minint, " - ", maxint)) + + property_df = data.frame(properties, values) + ]]></token> + + <token name="@CARDINAL_DESCRIPTION@"><![CDATA[ + Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. + `More information on Cardinal <http://cardinalmsi.org/>`_ + ]]></token> + <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" 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) + - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) + - m/z features outside the m/z range of the input file are ignored + + + :: + + m/z + 100.0 + 100.01 + 100.02 + ... + ... + + ]]></token> + <token name="@MZ_2COLS_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ + - Tabular file with m/z values: + + - One column with numeric m/z values (without empty fields or letters), another column with names for the m/z (m/z column can also be used as name) + - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) + - m/z features outside the m/z range of the input file are ignored + + + :: + + m/z name + 100.0 analyte1 + 100.01 analyte2 + 100.02 analyte3 + ... + ... + + ]]></token> + <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ + - Optional file with pixel coordinates and annotation: + + - Tabular file: One column with x values, one column wiht 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="Input file as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" + help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> + <param name="centroids" type="boolean" label="Is the input data centroided (picked)" 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> + </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> + </conditional> + </xml> + + <xml name="pdf_filename"> + <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + </param> + </xml> + + <xml name="sanitizer_multiple_digits"> + <sanitizer invalid_char=""> + <valid initial="string.digits"> + <add value=":" /> + <add value="," /> + </valid> + </sanitizer> + </xml> + + <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features"> + <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/> + <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/> + <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> + </xml> + + <xml name="reading_2_column_mz_tabular"> + <param name="calibrant_file" type="data" optional="true" format="tabular" + label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/> + <param name="mz_column" data_ref="calibrant_file" label="Column with m/z values" type="data_column"/> + <param name="name_column" data_ref="calibrant_file" label="Column with name of m/z values" type="data_column"/> + <param name="calibrant_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> + </xml> + + <xml name="reading_pixel_annotations"> + <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation" + help="Tabular file with three columns: x values, y values and pixel annotations"/> + <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/> + <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/> + <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/> + <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btv146</citation> + </citations> + </xml> + <xml name="infile_analyze75"> + <param name="infile" value="" ftype="analyze75"> + <composite_data value="Analyze75.hdr"/> + <composite_data value="Analyze75.img"/> + <composite_data value="Analyze75.t2m"/> + </param> + </xml> + <xml name="infile_imzml"> + <param name="infile" value="" ftype="imzml"> + <composite_data value="Example_Continuous.imzML"/> + <composite_data value="Example_Continuous.ibd"/> + </param> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spectra_plots.xml Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,455 @@ +<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.0"> + <description> + mass spectrometry imaging mass spectra plots + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="2.2.1">r-gridextra</requirement> + <requirement type="package" version="2.2.1">r-ggplot2</requirement> + <requirement type="package" version="0.5.0">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@ + +@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) + +## set NA to 0 otherwise plot function will not work + + spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero + +if (npeaks > 0){ + + pixeldf = data.frame(matrix(ncol = 2, nrow=0)) + + ############################# single pixel ################################ + ########################################################################### + + #if str( $pixel_conditional.pixel_type) == 'single_pixel': + print("single_pixel") + + #for $chosenpixel in $pixel_conditional.repeatpixel: + + pixelname = paste0("x = ", $chosenpixel.inputx,", ", "y = ", $chosenpixel.inputy) + pixelisvalid = as.character(pixelname %in% names(pixels(msidata))) + pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid)) + + ############################# II) control image #################### + + if (pixelisvalid == "TRUE"){ + print(pixelisvalid) + + image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1), + colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, + main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy)) + + abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth) + abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth) + + ##################### III) plot full mass spectrum ################# + + plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy)) + + ##################### IV) plot zoom-in mass spectrum ############### + + #if $chosenpixel.zoomedplot: + iData(msidata) <- iData(msidata)[] ## getting back data on disk + + #for $token in $chosenpixel.zoomedplot: + + minmasspixel = features(msidata, mz=$token.xlimmin) + maxmasspixel = features(msidata, mz=$token.xlimmax) + + plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy), + xlim= c($token.xlimmin,$token.xlimmax)) + + #end for + #end if + }else{ + print("The pixel coordinates did not correspond to a real pixel")} + #end for + + colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file") + + ############################# sample pixel ################################ + ########################################################################### + + #elif str( $pixel_conditional.pixel_type) == 'sample_pixel': + print("sample pixels") + + ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample) + + #if str($pixel_conditional.tabular_annotation.load_annotation) == 'yes_annotation': + + ## read and extract x,y,annotation information + input_tabular = read.delim("$pixel_conditional.tabular_annotation.annotation_file", header = $pixel_conditional.tabular_annotation.tabular_header, stringsAsFactors = FALSE) + annotation_input = input_tabular[,c($pixel_conditional.tabular_annotation.column_x, $pixel_conditional.tabular_annotation.column_y, $pixel_conditional.tabular_annotation.column_names)] + colnames(annotation_input) = c("x", "y", "annotation") + + ## merge with coordinate information of msidata + msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata))) + colnames(msidata_coordinates)[3] = "pixel_index" + merged_annotation = merge(msidata_coordinates, annotation_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 = as.factor(merged_annotation[,4]) + + #end if + + ##################### I) Sample: plot full mass spectrum ############## + + ## coloured plot with mean over all spectra with the same annotation, if no annotation is provided all pixels are considered as one sample + + if (!is.null(levels(msidata\$annotation))){ + print("annotated samples") + + ## 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 + } + + position_df = cbind(coord(msidata)[,1:2], as.factor(msidata\$annotation)) + colnames(position_df)[3] = "sample_name" + + 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 pixel 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 = 6))+ + guides(fill=guide_legend(ncol=4,byrow=TRUE)) + + coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass") + coord_labels\$file_number = 1:length(levels(position_df\$sample_name)) + + 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} + + spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero + plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE) + }else{ + spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero + plot(msidata, pixel=1:ncol(msidata), key=TRUE)} + + ##################### II) Sample: plot zoom-in mass spectrum ########## + + #if $pixel_conditional.zoomed_sample: + iData(msidata) <- iData(msidata)[] ## getting back data on disk + #for $token in $pixel_conditional.zoomed_sample: + print("zoomed sample pixels") + + minmasspixel = features(msidata, mz=$token.xlimmin) + maxmasspixel = features(msidata, mz=$token.xlimmax) + + ## coloured plot with mean over all spectra for annotation group, otherwise only 1 black plot + if (!is.null(levels(msidata\$annotation))){ + print("annotation samples") + plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), + xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation, + key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE) + }else{ + plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))} + + #end for + #end if + + if (!is.null(levels(msidata\$annotation))){ + pixeldf = data.frame(table(msidata\$annotation)) + }else{ + pixeldf = data.frame("$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="Select if you want to plot the mass spectrum of a single pixel or the average spectrum of all pixels of a sample"> + <option value="single_pixel" selected="True">Single pixel</option> + <option value="sample_pixel">Average spectrum for each sample</option> + </param> + <when value="single_pixel"> + <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20"> + <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/> + <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/> + <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, define m/z here" help="m/z will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/> + <param name="plusminusinDalton" value="0.25" type="float" label="m/z range for this m/z value" help="plusminus m/z window "/> + <param name="inputcolour" type="select" label="Select the colour for the lines at x and y position"> + <option value="white" selected="True">white</option> + <option value="black">black</option> + <option value="grey">grey</option> + <option value="blue">blue</option> + <option value="red">red</option> + <option value="green">green</option> + </param> + <param name="inputtype" type="select" label="Select the line type for the lines at x and y position"> + <option value="solid" selected="True">solid</option> + <option value="dashed">dashed</option> + <option value="dotted">dotted</option> + <option value="longdash">longdash</option> + </param> + <param name="inputwidth" type="integer" value="2" label="Select the width of the lines at x and y position"/> + <repeat name="zoomedplot" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50"> + <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/> + <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/> + </repeat> + </repeat> + </when> + <when value="sample_pixel"> + <conditional name="tabular_annotation"> + <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for spectra plots"> + <option value="no_annotation" selected="True">pixels belong into one group only</option> + <option value="yes_annotation">group pixels according to annotations</option> + </param> + <when value="yes_annotation"> + <expand macro="reading_pixel_annotations"/> + </when> + <when value="no_annotation"/> + </conditional> + <repeat name="zoomed_sample" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50"> + <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/> + <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/> + </repeat> + </when> + </conditional> + </inputs> + <outputs> + <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <expand macro="infile_imzml"/> + <conditional name="pixel_conditional"> + <param name="pixel_type" value="single_pixel"/> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.25"/> + <param name="inputx" value="3"/> + <param name="inputy" value="3"/> + <repeat name="zoomedplot"> + <param name="xlimmin" value="310"/> + <param name="xlimmax" value="320"/> + </repeat> + <repeat name="zoomedplot"> + <param name="xlimmin" value="350"/> + <param name="xlimmax" value="400"/> + </repeat> + <repeat name="zoomedplot"> + <param name="xlimmin" value="400"/> + <param name="xlimmax" value="420"/> + </repeat> + </repeat> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.25"/> + <param name="inputx" value="2"/> + <param name="inputy" value="2"/> + </repeat> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.25"/> + <param name="inputx" value="1"/> + <param name="inputy" value="1"/> + </repeat> + </conditional> + <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="single_pixel"/> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.25"/> + <param name="inputx" value="5"/> + <param name="inputy" value="2"/> + <repeat name="zoomedplot"> + <param name="xlimmin" value="840"/> + <param name="xlimmax" value="850"/> + </repeat> + </repeat> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.25"/> + <param name="inputx" value="2"/> + <param name="inputy" value="2"/> + </repeat> + </conditional> + <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="sample_pixel"/> + <conditional name="tabular_annotation"> + + <param name="load_annotation" value="yes_annotation"/> + <param name="annotation_file" value="annotations.tabular" ftype="tabular"/> + <param name="column_x" value="1"/> + <param name="column_y" value="2"/> + <param name="column_names" value="4"/> + <param name="tabular_header" value="TRUE"/> + + + + </conditional> + <repeat name="zoomed_sample"> + <param name="xlimmin" value="1250"/> + <param name="xlimmax" value="1270"/> + </repeat> + </conditional> + <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="sample_pixel"/> + <repeat name="zoomed_sample"> + <param name="xlimmin" value="350"/> + <param name="xlimmax" value="360"/> + </repeat> + </conditional> + <output name="plots" file="Plot_rdata.pdf" compare="sim_size"/> + </test> + <test> + <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> + <conditional name="pixel_conditional"> + <param name="pixel_type" value="single_pixel"/> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.1"/> + <param name="inputx" value="1"/> + <param name="inputy" value="1"/> + </repeat> + </conditional> + <output name="plots" file="Plot_empty_spectra.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@ + +**Options** + +- "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates + + - Enter the x and y coordinates of your pixel of interest + - To have a visual control for the selected pixel, a heatmap of a m/z of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an m/z of interest together with a m/z range and for the lines the colour and type. + - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot + +- "All pixels of a sample": Returns a full average mass spectrum plot with different colours for each pixel annotation group, without annotations the average of all pixels is plotted + + - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot + + +**Tip** + +- Corresponding m/z intensity pairs for single spectra can be obtained with the filtering tool option "ranges for x and y" and afterwards using the imzml tabular exporter tool +- Plots will only be drawn for pixels that exist in the MSI data, pixel that are outside the dataset will be "False" in the overview table on the last page of the pdf + + +**Output** + +- Pdf with the selected mass spectra plots and additional x-y grid plots + + +]]> + </help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/112_annotation_output.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,16 @@ +x y sample_name file_name column_name NA.x NA.y NA +1 1 msidata_1.RData file_one col1 NA NA NA +1 2 msidata_1.RData file_one col1 NA NA NA +1 3 msidata_1.RData file_one col1 NA NA NA +10 1 123_combined.RData file_two col3 NA NA NA +10 2 123_combined.RData file_two col3 NA NA NA +10 3 123_combined.RData file_two col3 NA NA NA +15 1 123_combined.RData file_three col3 NA NA NA +15 2 123_combined.RData file_three col3 NA NA NA +15 3 123_combined.RData file_three col3 NA NA NA +7 1 123_combined.RData file_one col1 NA NA NA +7 2 123_combined.RData file_one col1 NA NA NA +7 3 123_combined.RData file_one col1 NA NA NA +9 1 123_combined.RData file_two col2 NA NA NA +9 2 123_combined.RData file_two col2 NA NA NA +9 3 123_combined.RData file_two col2 NA NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/123_annotation.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,13 @@ +x y file_name column_name +1 1 file_one col1 +1 2 file_one col1 +1 3 file_one col1 +3 1 file_two col2 +3 2 file_two col2 +3 3 file_two col2 +4 1 file_two col3 +4 2 file_two col3 +4 3 file_two col3 +9 1 file_three col3 +9 2 file_three col3 +9 3 file_three col3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/123_annotation_output.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,13 @@ +x y sample_name file_name column_name NA.x NA.y NA +1 1 File1 file_one col1 NA NA NA +1 2 File1 file_one col1 NA NA NA +1 3 File1 file_one col1 NA NA NA +3 1 File2 file_two col2 NA NA NA +3 2 File2 file_two col2 NA NA NA +3 3 File2 file_two col2 NA NA NA +4 1 File2 file_two col3 NA NA NA +4 2 File2 file_two col3 NA NA NA +4 3 File2 file_two col3 NA NA NA +9 1 File3 file_three col3 NA NA NA +9 2 File3 file_three col3 NA NA NA +9 3 File3 file_three col3 NA NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12_annotation_output.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,10 @@ +x y sample_name file_name column_name NA.x NA.y NA +1 1 msidata_1.RData file_one col1 NA NA NA +1 2 msidata_1.RData file_one col1 NA NA NA +1 3 msidata_1.RData file_one col1 NA NA NA +7 1 msidata_2.RData file_two col2 NA NA NA +7 2 msidata_2.RData file_two col2 NA NA NA +7 3 msidata_2.RData file_two col2 NA NA NA +8 1 msidata_2.RData file_two col3 NA NA NA +8 2 msidata_2.RData file_two col3 NA NA NA +8 3 msidata_2.RData file_two col3 NA NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2123_annotation_output.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,19 @@ +x y sample_name +1 1 msidata_2.RData +2 1 msidata_2.RData +1 2 msidata_2.RData +2 2 msidata_2.RData +1 3 msidata_2.RData +2 3 msidata_2.RData +8 1 123_combined.RData +8 2 123_combined.RData +8 3 123_combined.RData +10 1 123_combined.RData +11 1 123_combined.RData +10 2 123_combined.RData +11 2 123_combined.RData +10 3 123_combined.RData +11 3 123_combined.RData +16 1 123_combined.RData +16 2 123_combined.RData +16 3 123_combined.RData
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/featuresofinterest5.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,31 @@ +115.333335876465 +115.416664123535 +115.5 +115.583335876465 +115.666664123535 +115.75 +115.833335876465 +115.916664123535 +116 +116.083335876465 +116.166664123535 +116.25 +116.333335876465 +116.416664123535 +116.5 +116.583335876465 +116.666664123535 +319.083343505859 +319.166687011719 +319.25 +319.333343505859 +319.416687011719 +319.5 +319.583343505859 +319.666687011719 +319.75 +319.8 +319.916687011719 +320 +320.0833435 +350
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputcalibrantfile1.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,3 @@ +101.5 +356.7 +555.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputcalibrantfile2.txt Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,3 @@ +869.51 mass1 +1111.1 mass2 +1296.7 mass3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,3 @@ +152 mass1 +328.9 mass2 +185.2 mass3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides2.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,4 @@ +854.5 +1111.1 +1296.7 +1305.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpixels_2column.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,6 @@ +1 A 1 +1 B 2 +1 C 3 +3 D 1 +3 E 2 +30 F 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int_matrix1.tabular Mon Oct 01 01:01:41 2018 -0400 @@ -0,0 +1,1200 @@ +mz_name xy_1_1 xy_2_1 xy_3_1 xy_1_2 xy_2_2 xy_3_2 xy_1_3 xy_2_3 xy_3_3 +mz_300.08 0 0 0 0 0.263692855834961 0 0 0 0 +mz_300.17 0 0 0 0 0.0258997213095427 0 0 0 0 +mz_300.25 0 1.59552115963635e-09 0 0 0 0 0 0 0 +mz_300.33 0 4.6339512782545e-10 0 0 0 0 0 0 0 +mz_300.42 0 3.61252902592035e-11 0 0 0 0 0 0 0 +mz_300.5 0 0 0 0 4.9563379434403e-05 0 0 0 0 +mz_300.58 0 0 0 0 3.55600786861032e-05 0 0 0 0 +mz_300.67 0 0 0 0 6.54657515042345e-06 0 0 0 0 +mz_300.75 0 1.1722580913788e-13 0 0 0 0 0 0 0 +mz_300.83 0 6.54903445384582e-14 0 0 0 0 0 0 0 +mz_300.92 0 1.07130575705038e-14 0 0 0 0 0 0 0 +mz_301 0 0 0 0 0 0 0 0 0 +mz_301.08 0 0 0 0 3.82026943412939e-09 0 0 0 0 +mz_301.17 0 0 0 0 1.14051934563264e-09 0 0 0 0 +mz_301.25 0 0 0 0 9.4434474129379e-11 0 0 0 0 +mz_301.33 0 7.46476736089292e-18 0 0 0 0 0 0 0 +mz_301.42 0 1.98718499598743e-18 0 0 0 0 0 0 0 +mz_301.5 0 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