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Changeset 2:17c54820f3be (2018-10-25)

Previous changeset 1:eaaa73b043e6 (2018-10-01) Next changeset 3:36d38d2cf88c (2019-02-15)

Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c

modified:
maldi_macros.xml
maldi_quant_peakdetection.xml
test-data/Preprocessing1_QC.pdf
test-data/Preprocessing2_QC.pdf
test-data/Preprocessing3_QC.pdf
test-data/outfile1.ibd
test-data/outfile1.imzML
test-data/outfile2.ibd
test-data/outfile2.imzML
test-data/outfile3.ibd
test-data/outfile3.imzML
test-data/peakdetection1_QC.pdf
test-data/peakdetection2_QC.pdf
test-data/peakdetection3_QC.pdf

added:
test-data/intensity_matrix4.tabular
test-data/masspeaks4.tabular
test-data/peakdetection4_QC.pdf
test-data/testfile_squares.rdata

diff -r eaaa73b043e6 -r 17c54820f3be maldi_macros.xml
--- a/maldi_macros.xml Mon Oct 01 01:09:43 2018 -0400
+++ b/maldi_macros.xml Thu Oct 25 07:32:17 2018 -0400

@@ -29,6 +29,7 @@
     <xml name="citation">
     <citations>
         <citation type="doi">10.1093/bioinformatics/bts447</citation>
+        <citation type="doi">10.1007/978-3-319-45809-0_6</citation>
     </citations>
     </xml>
</macros>

diff -r eaaa73b043e6 -r 17c54820f3be maldi_quant_peakdetection.xml
--- a/maldi_quant_peakdetection.xml Mon Oct 01 01:09:43 2018 -0400
+++ b/maldi_quant_peakdetection.xml Thu Oct 25 07:32:17 2018 -0400

[

b'@@ -1,4 +1,4 @@\n-<tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.1">\n+<tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.2">\n <description>\n Peak detection, binning and filtering for mass-spectrometry imaging data\n </description>\n@@ -31,8 +31,6 @@\n \n @R_IMPORTS@\n \n-\n-\n #if $restriction_conditional.restriction == \'restrict\':\n \n print(\'Reading mask region\')\n@@ -54,12 +52,14 @@\n print(\'imzML file\')\n #if str($centroids) == "TRUE"\n peaks <- importImzMl(\'infile.imzML\', centroided = $centroids)\n- pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")\n+ pixelnames = paste("xy", coordinates(peaks)[,1],coordinates(peaks)[,2], sep="_")\n+ coordinates_info = cbind(coordinates(peaks)[,1:2], c(1:length(peaks)))\n #else\n maldi_data <- importImzMl(\'infile.imzML\', centroided = $centroids)\n pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")\n+ coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))\n #end if\n- coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))\n+\n \n #elif $infile.ext == \'tabular\'\n print(\'tabular file\')\n@@ -84,8 +84,13 @@\n }\n msidata = loadRData(\'infile.RData\')\n centroided(msidata) = $centroids\n- pixelnames = gsub(", y = ", "_", names(Cardinal::pixels(msidata)))\n- pixelnames = gsub(" = ", "y_", pixelnames)\n+ ## change to correct pixelnames\n+\n+ x_coords = unlist(lapply(strsplit(names(Cardinal::pixels(msidata)), ","), `[[`, 1))\n+ y_coords = unlist(lapply(strsplit(names(Cardinal::pixels(msidata)), ","), `[[`, 2))\n+ x_coordinates = gsub("x = ","",x_coords)\n+ y_coordinates = gsub(" y = ","",y_coords)\n+ pixelnames = paste0("xy_", x_coordinates, "_", y_coordinates)\n \n cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])\n \n@@ -96,7 +101,6 @@\n for(number_spectra in 1:ncol(msidata)){\n maldi_data[[number_spectra]] = createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])\n coordinates_info = cbind(cardinal_coordinates, c(1:length(maldi_data)))}\n- coordinates_info = cbind(cardinal_coordinates, c(1:length(maldi_data)))\n }else{\n peaks = list()\n for (spectra in 1:ncol(msidata))\n@@ -107,15 +111,6 @@\n #end if\n #end if\n \n-\n-\n-\n-\n-\n-\n-\n-\n-\n ## default summarized = FALSE\n summarized_spectra = FALSE\n \n@@ -129,7 +124,7 @@\n title(main=paste("$filename"))\n \n ## plot input file spectrum: \n-#if str($centroids) == "TRUE"\n+#if $centroids:\n plot(peaks[[1]], main="First spectrum of input file")\n #else\n avgSpectra <- averageMassSpectra(maldi_data,method="mean")\n@@ -137,31 +132,26 @@\n #end if\n \n \n-\n-\n-\n-\n-\n-\n-\n ## QC numbers for input file\n #if str($centroids) == "TRUE"\n pixel_number = length(peaks)\n minmz = round(min(unlist(lapply(peaks,mass))), digits=4)\n maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)\n- maxfeatures = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)\n+ mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)\n medint = round(median(unlist(lapply(peaks,intensity))), digits=2)\n- inputdata = c(minmz, maxmz,maxfeatures, medint)\n- QC_numbers= data.frame(inputdata = c(minmz, maxmz,maxfeatures, medint))\n+ number_features = length(unique(unlist(lapply(peaks,mass))))\n+ inputdata = c(minmz, maxmz,number_features,mean_features, medint)\n+ QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint))\n vectorofactions = "inputdata"\n #else\n pixel_number = length(maldi_data)\n minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)\n maxmz '..b' mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]. A local maximum has to be the highest one in the given window to be recognized as peak.\n+ - Detect peaks on average mass spectra: Spectra with the same annotation (taken from the annotation tabular input) are averaged and peak picking is performed on the average spectrum of each annotation group. The exported imzML is empty and cannot be used for further analysis steps. The peaklist and intensity matrix outputs contain the annotation group names with their averaged intensity values. Filtering steps have to be done in the same run as the peak picking.\n+\n+\n - Monoisotopic peaks: detection of monoisotopic peaks\n-- Peak binning: After the alignment the peak positions (m/z) are very similar but not identical. The binning is needed to make similar peak m/z values identical.\n-- Peak filtering: Removal of less frequent peaks (either with a minimum ratio or with an absolute minimum number of spectra in which the peak has to occur)\n+\n+\n+\n+\n+- Peak binning: After the alignment the peak positions (m/z) are very similar but not identical. The binning is needed to make similar peak m/z values identical. The algorithm is based on the following workflow:\n+\n+ 1. Put all mass in a sorted vector.\n+ 2. Calculate differences between each neighbor.\n+ 3. Divide the mass vector at the largest gap (largest difference) and form a left and a right bin.\n+ 4. Rerun step 3 for the left and/or the right bin if they don\'t fulfill the following criteria:\n+\n+ - All peaks in a bin are near to the mean (abs(mass-meanMass)/meanMass < tolerance).\n+ - method == "strict": The bin doesn\'t contain two or more peaks of the same sample.\n+\n+\n+- Peak filtering: Removal of less frequent m/z features:\n+\n+ - minFrequency : between 0 and 1: m/z has to occur in 0 - 100% of all spectra; minNumber: m/z has to occur in at least this amount of spectra --> out of those two criteria the stricter value will be used\n+ - Group wise filtering with pixel annotations: \'Yes\' means that the filtering criteria are applied for each annotation group separately. \n+ - mergeWhitelists: \'Yes\' means that peaks that survive the filtering in one annotation group are also kept in other groups regardless if the filtering criteria are met in these groups\n+ - To filter data that was averaged before peak detection: Filtering has to be done in the same tool run as the peak detection. The filtering criteria are automatically applied per annotation group (Group wise filtering can be \'No\') and not per pixel. Example: to keep only m/z that were detected in at least half of all annotation groups set minFrequency to 0.5.\n \n \n **Output**\n \n-- centroided imzML file (processed or continuous), except for peak picking on the average of multiple spectra\n-- pdf with mass spectra plots after each preprocessing step\n+- centroided imzML file (processed or continuous), imzML file is empty when \'Detect peaks on average mass spectra\' is chosen.\n+- pdf with mass spectra plots after each preprocessing step and a table with key values after each preprocessing step\n - peak list (tabular file) with the columns "snr", "mass", "intensity" and "spectrum"\n-- tabular file with intensity matrix (m/z in rows and spectra in columns). If the input file was imzML in profile mode the intensities before peak picking are also stored in the matrix . For all other inputs not picked values are set to NA. For peak picking on the average of multiple spectra, each spectra group is a column with mean intensities for each m/z\n+- tabular file with intensity matrix (m/z in rows and spectra in columns). If the input file was imzML in profile mode the intensities before peak picking are also stored in the matrix . For all other inputs not picked values are set to NA. For peak picking on the average of multiple spectra, each spectra group is a column with mean intensities for each m/z.\n \n .. _MALDIquant: http://strimmerlab.org/software/maldiquant/\n \n'

diff -r eaaa73b043e6 -r 17c54820f3be test-data/Preprocessing1_QC.pdf

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diff -r eaaa73b043e6 -r 17c54820f3be test-data/Preprocessing2_QC.pdf

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diff -r eaaa73b043e6 -r 17c54820f3be test-data/Preprocessing3_QC.pdf

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diff -r eaaa73b043e6 -r 17c54820f3be test-data/intensity_matrix4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intensity_matrix4.tabular Thu Oct 25 07:32:17 2018 -0400

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diff -r eaaa73b043e6 -r 17c54820f3be test-data/masspeaks4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/masspeaks4.tabular Thu Oct 25 07:32:17 2018 -0400

b'@@ -0,0 +1,1862 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diff -r eaaa73b043e6 -r 17c54820f3be test-data/outfile1.ibd
--- a/test-data/outfile1.ibd Mon Oct 01 01:09:43 2018 -0400
+++ b/test-data/outfile1.ibd Thu Oct 25 07:32:17 2018 -0400

@@ -1,4 +1,4 @@
imzML file:
total 84
--rw-r--r-- 1 meli meli 67160 Aug 22 13:56 ibd
--rw-r--r-- 1 meli meli 15071 Aug 22 13:56 imzml
+-rw-r--r-- 1 meli meli 67160 Okt 24 10:12 ibd
+-rw-r--r-- 1 meli meli 15071 Okt 24 10:12 imzml

diff -r eaaa73b043e6 -r 17c54820f3be test-data/outfile1.imzML
--- a/test-data/outfile1.imzML Mon Oct 01 01:09:43 2018 -0400
+++ b/test-data/outfile1.imzML Thu Oct 25 07:32:17 2018 -0400

diff -r eaaa73b043e6 -r 17c54820f3be test-data/outfile2.ibd
--- a/test-data/outfile2.ibd Mon Oct 01 01:09:43 2018 -0400
+++ b/test-data/outfile2.ibd Thu Oct 25 07:32:17 2018 -0400

@@ -1,4 +1,4 @@
imzML file:
total 276
--rw-r--r-- 1 meli meli 268784 Aug 22 13:56 ibd
--rw-r--r-- 1 meli meli 9286 Aug 22 13:56 imzml
+-rw-r--r-- 1 meli meli 268784 Okt 24 10:12 ibd
+-rw-r--r-- 1 meli meli 9286 Okt 24 10:12 imzml

diff -r eaaa73b043e6 -r 17c54820f3be test-data/outfile2.imzML
--- a/test-data/outfile2.imzML Mon Oct 01 01:09:43 2018 -0400
+++ b/test-data/outfile2.imzML Thu Oct 25 07:32:17 2018 -0400

diff -r eaaa73b043e6 -r 17c54820f3be test-data/outfile3.ibd
--- a/test-data/outfile3.ibd Mon Oct 01 01:09:43 2018 -0400
+++ b/test-data/outfile3.ibd Thu Oct 25 07:32:17 2018 -0400

@@ -1,4 +1,4 @@
imzML file:
total 52
--rw-r--r-- 1 meli meli 38384 Aug 22 13:57 ibd
--rw-r--r-- 1 meli meli 9551 Aug 22 13:57 imzml
+-rw-r--r-- 1 meli meli 38384 Okt 24 10:13 ibd
+-rw-r--r-- 1 meli meli 9551 Okt 24 10:13 imzml

diff -r eaaa73b043e6 -r 17c54820f3be test-data/outfile3.imzML
--- a/test-data/outfile3.imzML Mon Oct 01 01:09:43 2018 -0400
+++ b/test-data/outfile3.imzML Thu Oct 25 07:32:17 2018 -0400

diff -r eaaa73b043e6 -r 17c54820f3be test-data/peakdetection1_QC.pdf

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diff -r eaaa73b043e6 -r 17c54820f3be test-data/peakdetection2_QC.pdf

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diff -r eaaa73b043e6 -r 17c54820f3be test-data/peakdetection3_QC.pdf

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diff -r eaaa73b043e6 -r 17c54820f3be test-data/peakdetection4_QC.pdf

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diff -r eaaa73b043e6 -r 17c54820f3be test-data/testfile_squares.rdata

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