Mercurial > repos > galaxyp > msi_ion_images
changeset 4:729a8bf3ffa9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_ion_images commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
| author | galaxyp |
|---|---|
| date | Mon, 28 May 2018 12:34:05 -0400 |
| parents | e045a8d295eb |
| children | a851b4e8fba7 |
| files | msi_ion_images.xml test-data/Analyze75.hdr test-data/Analyze75.img test-data/Analyze75.t2m test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_rdata.pdf test-data/LM8_file16.rdata test-data/empty_spectra.rdata test-data/inputpeptides2.tabular test-data/preprocessed.rdata test-data/preprocessing_results1.RData test-data/tabular_LM8file16.tabular test-data/tabular_analyze75.tabular test-data/tabular_imzml.tabular test-data/tabular_rdata.tabular |
| diffstat | 17 files changed, 89 insertions(+), 81 deletions(-) [+] |
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--- a/msi_ion_images.xml Mon Apr 23 17:16:47 2018 -0400 +++ b/msi_ion_images.xml Mon May 28 12:34:05 2018 -0400 @@ -1,22 +1,21 @@ -<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.7.0.3"> +<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.0"> <description> mass spectrometry imaging heatmaps </description> <requirements> - <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement> + <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> <requirement type="package" version="2.2.1">r-gridextra</requirement> - <requirement type="package" version="2.23-15">r-kernsmooth</requirement> <requirement type="package" version="0.20-35">r-lattice</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ #if $infile.ext == 'imzml' - cp '${infile.extra_files_path}/imzml' infile.imzML && - cp '${infile.extra_files_path}/ibd' infile.ibd && + ln -s '${infile.extra_files_path}/imzml' infile.imzML && + ln -s '${infile.extra_files_path}/ibd' infile.ibd && #elif $infile.ext == 'analyze75' - cp '${infile.extra_files_path}/hdr' infile.hdr && - cp '${infile.extra_files_path}/img' infile.img && - cp '${infile.extra_files_path}/t2m' infile.t2m && + 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 @@ -26,25 +25,25 @@ </command> <configfiles> <configfile name="MSI_heatmaps"><![CDATA[ -################################# load libraries and read file ######################### + +################################# load libraries and read file ################# library(Cardinal) library(gridExtra) -library(KernSmooth) library(lattice) ## Read MALDI Imaging dataset #if $infile.ext == 'imzml' - msidata = readMSIData('infile.imzML') + msidata = readImzML('infile') #elif $infile.ext == 'analyze75' - msidata = readMSIData('infile.hdr') + msidata = readAnalyze('infile') #else load('infile.RData') #end if -###################################### file properties in numbers ###################### +###################################### file properties in numbers ############## ## Number of features (mz) maxfeatures = length(features(msidata)) @@ -81,58 +80,64 @@ ## normalization if (length(processinginfo@normalization) == 0) { - normalizationinfo='FALSE' + normalizationinfo='FALSE' } else { - normalizationinfo=processinginfo@normalization + normalizationinfo=processinginfo@normalization } ## smoothing if (length(processinginfo@smoothing) == 0) { - smoothinginfo='FALSE' + smoothinginfo='FALSE' } else { - smoothinginfo=processinginfo@smoothing + smoothinginfo=processinginfo@smoothing } ## baseline if (length(processinginfo@baselineReduction) == 0) { - baselinereductioninfo='FALSE' + baselinereductioninfo='FALSE' } else { - baselinereductioninfo=processinginfo@baselineReduction + baselinereductioninfo=processinginfo@baselineReduction } ## peak picking if (length(processinginfo@peakPicking) == 0) { - peakpickinginfo='FALSE' + peakpickinginfo='FALSE' } else { - peakpickinginfo=processinginfo@peakPicking + peakpickinginfo=processinginfo@peakPicking } - -### Read tabular file with peptide masses for heatmap images: +##################################### read and filter input masses ############## input_list = read.delim("$massfile", header = FALSE, stringsAsFactors = FALSE) - if (ncol(input_list) == 1) - { - input_list = cbind(input_list, input_list) - } + +### in case input file had only one column with mz values but not names, duplicate mz values and use as names: - ### calculate how many input masses are valid: - inputmasses = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,] +if (ncol(input_list) == 1) +{ + input_list = cbind(input_list, input_list) +} - inputmz = inputmasses[,1] - inputnames = inputmasses[,2] +### calculate how many input masses are valid: +inputmasses = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,] + +inputmz = inputmasses[,1] +inputnames = inputmasses[,2] - if (nrow(input_list) == 1) - { +if (length(inputmz) == 1) +{ countpixels = sum(spectra(msidata)[features(msidata, mz = inputmz), ] >0) - }else { + percentpixels = round(countpixels/pixelcount*100, digits=1) + valuesdataframe = cbind(inputmz, cbind(countpixels, percentpixels)) + write.table(valuesdataframe, file="$pixel_count", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") +}else if (length(inputmz) >1) { countpixels = rowSums(spectra(msidata)[features(msidata, mz=inputmz),] >0) - } + percentpixels = round(countpixels/pixelcount*100, digits=1) + valuesdataframe = cbind(inputmz, cbind(countpixels, percentpixels)) + write.table(valuesdataframe, file="$pixel_count", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") +}else{ + valuesdataframe = data.frame(0,0) + write.table(valuesdataframe, file="$pixel_count", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") +} -percentpixels = round(countpixels/pixelcount*100, digits=1) -valuesdataframe = cbind(inputmz, cbind(countpixels, percentpixels)) - +############################ summarize file properties in numbers ############## -write.table(valuesdataframe, file="$pixel_count", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") - -colnames(input_list)[1:2] = c("mz", "name") properties = c("Number of mz features", "Range of mz values [Da]", "Number of pixels", @@ -170,43 +175,35 @@ property_df = data.frame(properties, values) - - -######################################## PDF ############################################# -########################################################################################## -########################################################################################## - +############################## PDF ############################################# pdf("heatmaps.pdf", fonts = "Times", pointsize = 12) plot(0,type='n',axes=FALSE,ann=FALSE) #if not $filename: #set $filename = $infile.display_name #end if -title(main=paste("Quality control of MSI data\n\n", "Filename:", "$filename")) +title(main=paste("\nHeatmap images\n\n", "Filename:\n", "$filename")) ############################# I) numbers #################################### -############################################################################# grid.table(property_df, rows= NULL) +############################# II) images #################################### + +### only plot images when file has peaks and valid input mz: + if (npeaks > 0) { - if (length(inputmz) != 0) { - for (mass in 1:length(inputmz)) { - - print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), - lattice=TRUE, ylim = c(maximumy+1,minimumy-1), plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", + lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", main= paste0(mass, ") ", inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)"))) } } else {print("The input masses were invalid")} - dev.off() - }else{ print("inputfile has no intensities > 0") dev.off() @@ -217,7 +214,7 @@ <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile 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="filename" type="text" value="" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name"/> - <param name="massfile" type="data" format="tabular" label="Text file with masses and names" + <param name="massfile" type="data" format="tabular" label="Tabular file with masses and names" help="first column mass (m/z), second column mass name, tab separated file"/> <param name="image_contrast" type="select" label="Select a contrast enhancement function for the heatmap images" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots"> <option value="none" selected="True">none</option> @@ -262,17 +259,17 @@ <output name="pixel_count" file="tabular_analyze75.tabular"/> </test> <test> - <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/> + <param name="infile" value="preprocessed.rdata" ftype="rdata"/> <param name="massfile" value="inputpeptides.tabular" ftype="tabular"/> - <param name="plusminus_dalton" value="0.1"/> + <param name="plusminus_dalton" value="0.5"/> <param name="filename" value="Testfile_rdata"/> <output name="plots" file="Heatmaps_rdata.pdf" compare="sim_size" delta="20000"/> <output name="pixel_count" file="tabular_rdata.tabular"/> </test> <test> - <param name="infile" value="LM8_file16.rdata" ftype="rdata"/> + <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> <param name="massfile" value="inputpeptides2.tabular" ftype="tabular"/> - <param name="plusminus_dalton" value="0.1"/> + <param name="plusminus_dalton" value="0.5"/> <param name="filename" value="Testfile_rdata"/> <output name="plots" file="Heatmaps_LM8_file16.pdf" compare="sim_size" delta="20000"/> <output name="pixel_count" file="tabular_LM8file16.tabular"/> @@ -280,26 +277,35 @@ </tests> <help><![CDATA[ -Heatmaps for different masses in mass-spectrometry imaging data as pdf output. +Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_ + +This tool uses the Cardinal image function to plot the intensity distribution of interesting masses of mass-spectrometry imaging data. Input data: 3 types of mass-spectrometry imaging data can be used: -- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_ +- 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 (with variable name "msidata", saved as .RData) -tabular file with masses: -- tab separated file (.tabular), datatype in Galaxy must be tabular (if Galaxy auto-detection was wrong, datatype can be changed by pressing the pen button) +Tabular file with masses: + +- tab separated file (.tabular), datatype in Galaxy must be tabular otherwise file will not appear in selection window (if Galaxy auto-detection was wrong, datatype can be changed by pressing button with the pen (edit attributes)) - first column must contain masses (separate point numbers by point, not comma) - optionally a second column with names for the masses can be provided -- no empty fields or letters are allowed (tool crashes with empty fields and a single letter prohibits generation of images) +- no empty fields or letters are allowed in the first column + +Output: -Trouble shooting: -- no heatmaps are plotted when tabular file contains letters or point numbers with commas or when the input MSI file had no intensities > 0 -- contrast enhance functions need masses with intensities > 0 in about 1.5% of all pixels - tool crashes when contrast enhance is used on too few intensities +- Pdf with the heatmap images +- Tabular with masses that were in the mass range and their occurence over all pixels (absolute and in %) +Troubleshooting: + +- no heatmaps are plotted when tabular file doesn't fulfill the criteria described above +- no heatmaps are plotted when the input mass spectrometry imaging file has no intensities > 0 +- out of thetabular file only masses with > 1.5-2% pixel coverage can be used with the contrast enhance and image smoothing functions, as both crash when a mass has not enough intensity values ]]> </help>
--- a/test-data/inputpeptides2.tabular Mon Apr 23 17:16:47 2018 -0400 +++ b/test-data/inputpeptides2.tabular Mon May 28 12:34:05 2018 -0400 @@ -1,1 +1,4 @@ 854.5 +1111.1 +1296.7 +1305.1
--- a/test-data/tabular_LM8file16.tabular Mon Apr 23 17:16:47 2018 -0400 +++ b/test-data/tabular_LM8file16.tabular Mon May 28 12:34:05 2018 -0400 @@ -1,2 +1,2 @@ - inputmz countpixels percentpixels -1 854.5 0 0 +inputmz countpixels percentpixels +1111.1 0 0
--- a/test-data/tabular_analyze75.tabular Mon Apr 23 17:16:47 2018 -0400 +++ b/test-data/tabular_analyze75.tabular Mon May 28 12:34:05 2018 -0400 @@ -1,2 +1,3 @@ - inputmz countpixels percentpixels -1 854.5 2 22.2 +inputmz countpixels percentpixels +1296.7 9 100 +1305.1 9 100
--- a/test-data/tabular_imzml.tabular Mon Apr 23 17:16:47 2018 -0400 +++ b/test-data/tabular_imzml.tabular Mon May 28 12:34:05 2018 -0400 @@ -1,4 +1,4 @@ - inputmz countpixels percentpixels -1 152 9 100 -2 328.9 9 100 -3 185.2 6 66.7 +inputmz countpixels percentpixels +152 9 100 +328.9 9 100 +185.2 6 66.7