Mercurial > repos > galaxyp > msi_filtering
changeset 5:1845ec48ad00 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
| author | galaxyp |
|---|---|
| date | Fri, 06 Jul 2018 14:10:55 -0400 |
| parents | 5024bfc81c37 |
| children | c7c91ceeffcd |
| files | msi_filtering.xml test-data/analyze75_filtered2.pdf test-data/analyze_filtered.RData test-data/analyze_filtered.pdf test-data/analyze_filteredoutside.RData test-data/analyze_matrix.tabular test-data/imzml_filtered.RData test-data/imzml_filtered.pdf test-data/imzml_filtered2.RData test-data/imzml_filtered2.pdf test-data/imzml_filtered3.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.RData test-data/imzml_filtered4.pdf test-data/imzml_filtered5.RData test-data/imzml_filtered5.pdf test-data/imzml_matrix3.tabular test-data/rdata_matrix.tabular |
| diffstat | 18 files changed, 293 insertions(+), 265 deletions(-) [+] |
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--- a/msi_filtering.xml Tue Jun 19 18:04:51 2018 -0400 +++ b/msi_filtering.xml Fri Jul 06 14:10:55 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.2"> +<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.3"> <description>tool for filtering mass spectrometry imaging data</description> <requirements> <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> @@ -33,343 +33,371 @@ library(Cardinal) library(gridExtra) + #if $infile.ext == 'imzml' - msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") + #if str($processed_cond.processed_file) == "processed": + msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") + #else + msidata <- readImzML('infile') + #end if #elif $infile.ext == 'analyze75' msidata = readAnalyze('infile') #else load('infile.RData') #end if + ########################### optional QC numbers ######################## -#if $outputs.outputs_select == "quality_control": +if (sum(spectra(msidata)[]>0, na.rm=TRUE) > 0) +{ + #if $outputs.outputs_select == "quality_control": - ## Number of features (m/z) - maxfeatures = length(features(msidata)) - ## Range m/z - 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]) - ## Number of intensities > 0 - npeaks= sum(spectra(msidata)[]>0) - ## Spectra multiplied with m/z (potential number of peaks) - numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) - ## Percentage of intensities > 0 - percpeaks = round(npeaks/numpeaks*100, digits=2) - ## Number of empty TICs - TICs = colSums(spectra(msidata)[]) - NumemptyTIC = sum(TICs == 0) - ## median TIC - medint = round(median(TICs), digits=2) - ## Store features for QC plot - featuresinfile = mz(msidata) + ## Number of features (m/z) + maxfeatures = length(features(msidata)) + ## Range m/z + 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]) + ## Number of intensities > 0 + npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE) + ## Spectra multiplied with m/z (potential number of peaks) + numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) + ## Percentage of intensities > 0 + percpeaks = round(npeaks/numpeaks*100, digits=2) + ## Number of empty TICs + TICs = colSums(spectra(msidata)[], na.rm=TRUE) + NumemptyTIC = sum(TICs == 0) + ## median TIC + medint = round(median(TICs), digits=2) + ## Store features for QC plot + featuresinfile = mz(msidata) -#end if + #end if -###################################### Filtering of pixels ##################### -################################################################################ + ###################################### Filtering of pixels ##################### + ################################################################################ -#################### Pixels in the one column format "x=,y=" ##################### + #################### Pixels in the one column format "x=,y=" ##################### -#if str($pixels_cond.pixel_filtering) == "single_column": - print("single column") + #if str($pixels_cond.pixel_filtering) == "single_column": + print("single column") - input_list = read.delim("$pixels_cond.single_pixels", header = FALSE, stringsAsFactors = FALSE) - numberpixels = length(input_list[,$pixels_cond.pixel_column]) - valid_entries = input_list[,$pixels_cond.pixel_column] %in% names(pixels(msidata)) - validpixels = sum(valid_entries) + input_list = read.delim("$pixels_cond.single_pixels", header = FALSE, stringsAsFactors = FALSE) + numberpixels = length(input_list[,$pixels_cond.pixel_column]) + valid_entries = input_list[,$pixels_cond.pixel_column] %in% names(pixels(msidata)) + validpixels = sum(valid_entries) - if (validpixels != 0){ - pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[valid_entries,$pixels_cond.pixel_column]] - msidata = msidata[,pixelsofinterest] - }else{ - msidata = msidata[,0] - validpixels=0} + if (validpixels != 0){ + pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[valid_entries,$pixels_cond.pixel_column]] + msidata = msidata[,pixelsofinterest] + }else{ + msidata = msidata[,0] + validpixels=0} + + ############ Pixels in two columns format: x and y in different columns ############# -############ Pixels in two columns format: x and y in different columns ############# + #elif str($pixels_cond.pixel_filtering) == "two_columns": + print("two columns") -#elif str($pixels_cond.pixel_filtering) == "two_columns": - print("two columns") - - input_list = read.delim("$pixels_cond.two_columns_pixel", header = FALSE, - stringsAsFactors = FALSE) - numberpixels = length(input_list[,$pixels_cond.pixel_column_x]) + input_list = read.delim("$pixels_cond.two_columns_pixel", header = FALSE, + stringsAsFactors = FALSE) + numberpixels = length(input_list[,$pixels_cond.pixel_column_x]) - inputpixel_x = input_list[,$pixels_cond.pixel_column_x] - inputpixel_y = input_list[,$pixels_cond.pixel_column_y] - inputpixels = cbind(inputpixel_x, inputpixel_y) - colnames(inputpixels) = c("x", "y") - valid_rows = merge(inputpixels, coord(msidata)[,1:2]) - validpixels = nrow(valid_rows) + inputpixel_x = input_list[,$pixels_cond.pixel_column_x] + inputpixel_y = input_list[,$pixels_cond.pixel_column_y] + inputpixels = cbind(inputpixel_x, inputpixel_y) + colnames(inputpixels) = c("x", "y") + valid_rows = merge(inputpixels, coord(msidata)[,1:2]) + validpixels = nrow(valid_rows) - if (validpixels != 0){ - pixelvector = character() - for (pixel in 1:nrow(valid_rows)){ - pixelvector[pixel] = paste0("x = ", valid_rows[pixel,1],", ", "y = ", valid_rows[pixel,2])} - pixelsofinterest= pixels(msidata)[names(pixels(msidata)) %in% pixelvector] - msidata = msidata[,pixelsofinterest] - }else{ - validpixels=0} + if (validpixels != 0){ + pixelvector = character() + for (pixel in 1:nrow(valid_rows)){ + pixelvector[pixel] = paste0("x = ", valid_rows[pixel,1],", ", "y = ", valid_rows[pixel,2])} + pixelsofinterest= pixels(msidata)[names(pixels(msidata)) %in% pixelvector] + msidata = msidata[,pixelsofinterest] + }else{ + validpixels=0} + + ########### Pixels wihin x and y minima and maxima are kept ################### -########### Pixels wihin x and y minima and maxima are kept ################### - -#elif str($pixels_cond.pixel_filtering) == "pixel_range": - print("pixel range") + #elif str($pixels_cond.pixel_filtering) == "pixel_range": + print("pixel range") - numberpixels = "range" - validpixels = "range" + numberpixels = "range" + validpixels = "range" -## only filter pixels if at least one pixel will be left + ## only filter pixels if at least one pixel will be left + + if (sum(coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range) > 0 & sum(coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range) > 0){ - if (sum(coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range) > 0 & sum(coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range) > 0){ - msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range] - msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range] - }else{ - msidata = msidata[,0] - print("no valid pixel found")} + msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range] + msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range] + }else{ + msidata = msidata[,0] + print("no valid pixel found")} + + #elif str($pixels_cond.pixel_filtering) == "none": + print("no pixel filtering") -#elif str($pixels_cond.pixel_filtering) == "none": - print("no pixel filtering") + numberpixels = 0 + validpixels = 0 + + #end if - numberpixels = 0 - validpixels = 0 -#end if +}else{ + print("Inputfile has no intensities > 0") +} ###################################### filtering of features ###################### ################################################################################## ######################## Keep m/z from tabular file ######################### -#if str($features_cond.features_filtering) == "features_list": - print("feature list") +if (sum(spectra(msidata)[], na.rm=TRUE) > 0){ - input_features = read.delim("$inputfeatures", header = FALSE, stringsAsFactors = FALSE) - startingrow = $features_cond.feature_header+1 - extracted_features = input_features[startingrow:nrow(input_features),$features_cond.feature_column] - numberfeatures = length(extracted_features) - - if (grepl("m/z = ", input_features[startingrow,$features_cond.feature_column])==FALSE){ + #if str($features_cond.features_filtering) == "features_list": + print("feature list") -### if input is in numeric format - if (class(extracted_features) == "numeric"){ - ### max digits given in the input file will be used to match m/z - max_digits = max(nchar(matrix(unlist(strsplit(as.character(extracted_features), "\\.")), ncol=2, byrow=TRUE)[,2])) - validfeatures = extracted_features %in% round(mz(msidata),max_digits) - featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% extracted_features[validfeatures]] - validmz = length(unique(featuresofinterest)) - }else{ - validmz = 0 - featuresofinterest = 0} + input_features = read.delim("$inputfeatures", header = FALSE, stringsAsFactors = FALSE) + startingrow = $features_cond.feature_header+1 + extracted_features = input_features[startingrow:nrow(input_features),$features_cond.feature_column] + numberfeatures = length(extracted_features) -### if input is already in character format (m/z = 800.01) + if (grepl("m/z = ", input_features[startingrow,$features_cond.feature_column])==FALSE){ - }else{ - validfeatures = extracted_features %in% names(features(msidata)) - featuresofinterest = features(msidata)[names(features(msidata)) %in% extracted_features[validfeatures]] - validmz = sum(validfeatures)} + ### if input is in numeric format + if (class(extracted_features) == "numeric"){ + ### max digits given in the input file will be used to match m/z + max_digits = max(nchar(matrix(unlist(strsplit(as.character(extracted_features), "\\.")), ncol=2, byrow=TRUE)[,2])) + validfeatures = extracted_features %in% round(mz(msidata),max_digits) + featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% extracted_features[validfeatures]] + validmz = length(unique(featuresofinterest)) + }else{ + validmz = 0 + featuresofinterest = 0} -### filter msidata for valid features - - msidata = msidata[featuresofinterest,] - -############### features within a given range are kept ######################### + ### if input is already in character format (m/z = 800.01) -#elif str($features_cond.features_filtering) == "features_range": - print("feature range") + }else{ + validfeatures = extracted_features %in% names(features(msidata)) + featuresofinterest = features(msidata)[names(features(msidata)) %in% extracted_features[validfeatures]] + validmz = sum(validfeatures)} - numberfeatures = "range" - validmz = "range" + ### filter msidata for valid features - if (sum(mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz)> 0){ - msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,] - }else{ - msidata = msidata[0,] - print("no valid mz range")} + msidata = msidata[featuresofinterest,] + + ############### features within a given range are kept ######################### + + #elif str($features_cond.features_filtering) == "features_range": + print("feature range") + + numberfeatures = "range" + validmz = "range" -############### Remove m/z from tabular file ######################### + if (sum(mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz)> 0){ + msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,] + }else{ + msidata = msidata[0,] + print("no valid mz range")} -#elif str($features_cond.features_filtering) == "remove_features": - print("remove features") - -### Tabular file contains mz either as numbers or in the format mz = 800.01 + ############### Remove m/z from tabular file ######################### - input_features = read.delim("$inputfeatures_removal", header = FALSE, stringsAsFactors = FALSE) - startingrow = $features_cond.removal_header+1 - extracted_features = input_features[startingrow:nrow(input_features),$features_cond.removal_column] - numberfeatures = length(extracted_features) + #elif str($features_cond.features_filtering) == "remove_features": + print("remove features") - if (grepl("m/z = ", input_features[startingrow,$features_cond.removal_column])==TRUE){ + ### Tabular file contains mz either as numbers or in the format mz = 800.01 -### if input is mz = 800 character format - print("input is in format mz = 400") - validfeatures = extracted_features %in% names(features(msidata)) - validmz = sum(validfeatures) - filtered_features = features(msidata)[names(features(msidata)) %in% extracted_features[validfeatures]] - featuresofinterest = mz(msidata)[filtered_features] + input_features = read.delim("$inputfeatures_removal", header = FALSE, stringsAsFactors = FALSE) + startingrow = $features_cond.removal_header+1 + extracted_features = input_features[startingrow:nrow(input_features),$features_cond.removal_column] + numberfeatures = length(extracted_features) + + if (grepl("m/z = ", input_features[startingrow,$features_cond.removal_column])==TRUE){ -### if input is numeric: - }else{ - if (class(extracted_features) == "numeric"){ - print("input is numeric") - featuresofinterest = extracted_features - validmz = sum(featuresofinterest <= max(mz(msidata))& featuresofinterest >= min(mz(msidata))) - }else{featuresofinterest = 0 - validmz = 0} - } - -### Here starts removal of features: + ### if input is mz = 800 character format + print("input is in format mz = 400") + validfeatures = extracted_features %in% names(features(msidata)) + validmz = sum(validfeatures) + filtered_features = features(msidata)[names(features(msidata)) %in% extracted_features[validfeatures]] + featuresofinterest = mz(msidata)[filtered_features] - plusminus = $features_cond.removal_plusminus + ### if input is numeric: + }else{ + if (class(extracted_features) == "numeric"){ + print("input is numeric") + featuresofinterest = extracted_features + validmz = sum(featuresofinterest <= max(mz(msidata))& featuresofinterest >= min(mz(msidata))) + }else{featuresofinterest = 0 + validmz = 0} + } + + ### Here starts removal of features: - mass_to_remove = numeric() - if (sum(featuresofinterest) > 0){ - for (masses in featuresofinterest){ - #if str($features_cond.units_removal) == "ppm": - plusminus = masses * $features_cond.removal_plusminus/1000000 - #end if - current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus)) - mass_to_remove = append(mass_to_remove, current_mass)} - msidata= msidata[-mass_to_remove, ] - }else{print("No features were removed as they were not fitting to m/z values and/or range")} + plusminus = $features_cond.removal_plusminus + + mass_to_remove = numeric() + if (sum(featuresofinterest) > 0){ + for (masses in featuresofinterest){ + #if str($features_cond.units_removal) == "ppm": + plusminus = masses * $features_cond.removal_plusminus/1000000 + #end if + current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus)) + mass_to_remove = append(mass_to_remove, current_mass)} + msidata= msidata[-mass_to_remove, ] + }else{print("No features were removed as they were not fitting to m/z values and/or range")} -#elif str($features_cond.features_filtering) == "none": + #elif str($features_cond.features_filtering) == "none": - print("no feature filtering") - validmz = 0 - numberfeatures = 0 + print("no feature filtering") + validmz = 0 + numberfeatures = 0 -#end if + #end if -## save msidata as Rfile -save(msidata, file="$msidata_filtered") + ## save msidata as Rfile + save(msidata, file="$msidata_filtered") -#################### optional QC numbers ####################### + #################### optional QC numbers ####################### -#if $outputs.outputs_select == "quality_control": + #if $outputs.outputs_select == "quality_control": - ## Number of features (m/z) - maxfeatures2 = length(features(msidata)) - ## Range m/z - minmz2 = round(min(mz(msidata)), digits=2) - maxmz2 = round(max(mz(msidata)), digits=2) - ## Number of spectra (pixels) - pixelcount2 = length(pixels(msidata)) - ## Range x coordinates - minimumx2 = min(coord(msidata)[,1]) - maximumx2 = max(coord(msidata)[,1]) - ## Range y coordinates - minimumy2 = min(coord(msidata)[,2]) - maximumy2 = max(coord(msidata)[,2]) - ## Number of intensities > 0 - npeaks2= sum(spectra(msidata)[]>0) - ## Spectra multiplied with m/z (potential number of peaks) - numpeaks2 = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) - ## Percentage of intensities > 0 - percpeaks2 = round(npeaks2/numpeaks2*100, digits=2) - ## Number of empty TICs - TICs2 = colSums(spectra(msidata)[]) - NumemptyTIC2 = sum(TICs2 == 0) - ## median TIC - medint2 = round(median(TICs2), digits=2) + ## Number of features (m/z) + maxfeatures2 = length(features(msidata)) + ## Range m/z + minmz2 = round(min(mz(msidata)), digits=2) + maxmz2 = round(max(mz(msidata)), digits=2) + ## Number of spectra (pixels) + pixelcount2 = length(pixels(msidata)) + ## Range x coordinates + minimumx2 = min(coord(msidata)[,1]) + maximumx2 = max(coord(msidata)[,1]) + ## Range y coordinates + minimumy2 = min(coord(msidata)[,2]) + maximumy2 = max(coord(msidata)[,2]) + ## Number of intensities > 0 + npeaks2= sum(spectra(msidata)[]>0, na.rm=TRUE) + ## Spectra multiplied with m/z (potential number of peaks) + numpeaks2 = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) + ## Percentage of intensities > 0 + percpeaks2 = round(npeaks2/numpeaks2*100, digits=2) + ## Number of empty TICs + TICs2 = colSums(spectra(msidata)[], na.rm=TRUE) + NumemptyTIC2 = sum(TICs2 == 0) + ## median TIC + medint2 = round(median(TICs2), digits=2) - properties = c("Number of m/z features", - "Range of m/z values", - "Number of pixels", - "Range of x coordinates", - "Range of y coordinates", - "Intensities > 0", - "Median TIC per pixel", - "Number of zero TICs", - "pixel overview", - "feature overview") + properties = c("Number of m/z features", + "Range of m/z values", + "Number of pixels", + "Range of x coordinates", + "Range of y coordinates", + "Intensities > 0", + "Median TIC per pixel", + "Number of zero TICs", + "pixel overview", + "feature overview") - before = c(paste0(maxfeatures), - paste0(minmz, " - ", maxmz), - paste0(pixelcount), - paste0(minimumx, " - ", maximumx), - paste0(minimumy, " - ", maximumy), - paste0(percpeaks, " %"), - paste0(medint), - paste0(NumemptyTIC), - paste0("input pixels: ", numberpixels), - paste0("input mz: ", numberfeatures)) + before = c(paste0(maxfeatures), + paste0(minmz, " - ", maxmz), + paste0(pixelcount), + paste0(minimumx, " - ", maximumx), + paste0(minimumy, " - ", maximumy), + paste0(percpeaks, " %"), + paste0(medint), + paste0(NumemptyTIC), + paste0("input pixels: ", numberpixels), + paste0("input mz: ", numberfeatures)) - filtered = c(paste0(maxfeatures2), - paste0(minmz2, " - ", maxmz2), - paste0(pixelcount2), - paste0(minimumx2, " - ", maximumx2), - paste0(minimumy2, " - ", maximumy2), - paste0(percpeaks2, " %"), - paste0(medint2), - paste0(NumemptyTIC2), - paste0("valid pixels: ", validpixels), - paste0("valid mz: ", validmz)) + filtered = c(paste0(maxfeatures2), + paste0(minmz2, " - ", maxmz2), + paste0(pixelcount2), + paste0(minimumx2, " - ", maximumx2), + paste0(minimumy2, " - ", maximumy2), + paste0(percpeaks2, " %"), + paste0(medint2), + paste0(NumemptyTIC2), + paste0("valid pixels: ", validpixels), + paste0("valid mz: ", validmz)) - property_df = data.frame(properties, before, filtered) + property_df = data.frame(properties, before, filtered) -############################### optional PDF QC ################################ + ############################### optional PDF QC ################################ - pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12) - plot(0,type='n',axes=FALSE,ann=FALSE) - title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name")) - grid.table(property_df, rows= NULL) + pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12) + plot(0,type='n',axes=FALSE,ann=FALSE) + title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name")) + grid.table(property_df, rows= NULL) - ### heatmap image as visual pixel control - if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){ - image(msidata, mz=$outputs.inputmz, plusminus = $outputs.plusminus_dalton, contrast.enhance = "none", - main= paste0($outputs.inputmz," ± ", $outputs.plusminus_dalton, " Da"), ylim = c(maximumy2+0.2*maximumy2,minimumy2-0.2*minimumy2)) + ### heatmap image as visual pixel control + if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){ + image(msidata, mz=$outputs.inputmz, plusminus = $outputs.plusminus_dalton, contrast.enhance = "none", + main= paste0($outputs.inputmz," ± ", $outputs.plusminus_dalton, " Da"), ylim = c(maximumy2+0.2*maximumy2,minimumy2-0.2*minimumy2)) - ### control features which are removed - hist(mz(msidata), xlab="m/z", main="Kept m/z values") - #if str($features_cond.features_filtering) == "none": - print("no difference histogram as no m/z filtering took place") - #else: - hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values") - #end if - }else{ - print("file has no features or pixels left")} + ### control features which are removed + hist(mz(msidata), xlab="m/z", main="Kept m/z values") + #if str($features_cond.features_filtering) == "none": + print("no difference histogram as no m/z filtering took place") + #else: - dev.off() + if (isTRUE(all.equal(featuresinfile, mz(msidata)))){ + print("No difference in m/z values before and after filtering, no histogram drawn") + }else{ + hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values")} + #end if + }else{ + print("file has no features or pixels left")} -#end if + dev.off() + + #end if -############################### optional intensity matrix ###################### + ############################### optional intensity matrix ###################### -#if $output_matrix: + #if $output_matrix: -if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){ - spectramatrix = spectra(msidata) - rownames(spectramatrix) = mz(msidata) - newmatrix = rbind(pixels(msidata), spectramatrix) - write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") + spectramatrix = spectra(msidata)[] + spectramatrix = cbind(mz(msidata),spectramatrix) + newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix) + write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t") + + #end if + }else{ - print("file has no features or pixels left")} - -#end if - - + print("Inputfile or file filtered for pixels has no intensities > 0") +} ]]></configfile> </configfiles> <inputs> <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="accuracy" type="float" value="50" label="Only for processed imzML files: enter 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="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> - <option value="mz" >mz</option> - <option value="ppm" selected="True" >ppm</option> - </param> + <conditional name="processed_cond"> + <param name="processed_file" type="select" label="Is the input file a processed imzML file "> + <option value="no_processed" selected="True">not a processed imzML</option> + <option value="processed">processed imzML</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> <conditional name="pixels_cond"> <param name="pixel_filtering" type="select" label="Select pixel filtering option"> <option value="none" selected="True">none</option> @@ -605,7 +633,7 @@ - pixel filtering: can use a tabular file containing x and y coordinates or by defining a range for x and y by hand - m/z feature filtering: can use a tabular file containing m/z of interest or by defining a range for the m/z values (! numeric input will be rounded to 2 digits before matching to m/z!) -- m/z feature removing: infering m/z such as matrix contaminants can be removed by specifying their m/z in a tabular file and optionally set a window (window in ppm or Da in which peaks should be removed) +- m/z feature removing: infering m/z such as matrix contaminants can be removed by specifying their m/z in a tabular file and optionally set a window (window in ppm or m/z in which peaks should be removed) Output:
--- a/test-data/analyze_matrix.tabular Tue Jun 19 18:04:51 2018 -0400 +++ b/test-data/analyze_matrix.tabular Fri Jul 06 14:10:55 2018 -0400 @@ -1,4 +1,4 @@ - x = 1, y = 1 x = 1, y = 2 x = 3, y = 2 x = 1, y = 3 +mz | spectra x = 1, y = 1 x = 1, y = 2 x = 3, y = 2 x = 1, y = 3 1201.3349609375 14 12 9 14 1201.37634277344 17 21 11 20 1201.45910644531 22 18 18 22
--- a/test-data/imzml_matrix3.tabular Tue Jun 19 18:04:51 2018 -0400 +++ b/test-data/imzml_matrix3.tabular Fri Jul 06 14:10:55 2018 -0400 @@ -1,4 +1,4 @@ - x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 +mz | spectra x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 350 0 1.18586093356332e-26 7.10052307988494e-32 350.083343505859 0 1.41173515299902e-27 0 350.166687011719 5.94295388740686e-26 0 0
--- a/test-data/rdata_matrix.tabular Tue Jun 19 18:04:51 2018 -0400 +++ b/test-data/rdata_matrix.tabular Fri Jul 06 14:10:55 2018 -0400 @@ -1,4 +1,4 @@ - x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3 +mz | spectra x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3 200.083343505859 46.3652739153013 0 9.17289559719717e-05 0 0 0 1.29693162341385 0 1.78496635304646e-05 200.16667175293 22.4757921402152 0 0 5.8254927250654e-08 0 0 0 0 0 200.25 38.2466047658708 0 0 3.59839441365526e-08 0 0 0 8.34774930605485e-08 0 @@ -1284,7 +1284,7 @@ 306.916687011719 2.2031921865656e-20 0 0 40.486491025881 0.122643497590777 0 0 13.9093994733916 1.33194911356925 307 3.66559723583287e-21 6.29805161971829e-08 0 21.0239930982532 10.627775415752 0 0 4.96484942878176 0.176964102474979 307.083343505859 0 3.73410909186729e-08 0 18.3089774049594 27.7952080229158 0 0 0.316976571174355 22.5696806926193 -307.166687011719 0 6.30821295171180e-09 6.89037923740047e-08 4.04689979105835 11.095809382106 0 1.35488457018982e-15 0 49.9638795251359 +307.166687011719 0 6.3082129517118e-09 6.89037923740047e-08 4.04689979105835 11.095809382106 0 1.35488457018982e-15 0 49.9638795251359 307.25 0 0 2.43069082104212e-08 0 1.40410351777257 0 7.73638174561519e-16 0 19.1456170512867 307.333343505859 0 0 2.66083795902358e-09 0 0 0 1.28100418575255e-16 0 2.34396309903659 307.416687011719 2.49160463062269e-24 0 0 0 0 0 0 0.00148088913948611 0