| Previous changeset 2:17c54820f3be (2018-10-25) Next changeset 4:e9300ef37403 (2019-03-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 |
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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/outfile2.ibd test-data/outfile3.ibd test-data/peakdetection1_QC.pdf test-data/peakdetection2_QC.pdf test-data/peakdetection3_QC.pdf test-data/peakdetection4_QC.pdf |
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added:
test-data/inputpeptides.tabular test-data/outfile1.imzml test-data/outfile2.imzml test-data/outfile3.imzml test-data/peak_detection1.imzml.txt test-data/peak_detection2.ibd test-data/peak_detection2.imzml test-data/peak_detection2.imzml.txt test-data/peak_detection3.ibd test-data/peak_detection3.imzml test-data/peak_detection3.imzml.txt test-data/peak_detection4.ibd test-data/peak_detection4.imzml test-data/peak_detection4.imzml.txt test-data/preprocessing1.imzml.txt test-data/preprocessing2.imzml.txt test-data/preprocessing3.imzml.txt |
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removed:
test-data/align_reference_test2.tabular test-data/outfile1.imzML test-data/outfile2.imzML test-data/outfile3.imzML |
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| diff -r 17c54820f3be -r 36d38d2cf88c maldi_macros.xml --- a/maldi_macros.xml Thu Oct 25 07:32:17 2018 -0400 +++ b/maldi_macros.xml Fri Feb 15 10:26:45 2019 -0500 |
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| @@ -18,11 +18,12 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> + <requirement type="package" version="3.5.1">r-base</requirement> + <requirement type="package" version="1.12.1">bioconductor-cardinal</requirement> <requirement type="package" version="0.11.5">r-maldiquantforeign</requirement> <requirement type="package" version="1.18">r-maldiquant</requirement> - <requirement type="package" version="2.2.1">r-ggplot2</requirement> - <requirement type="package" version="2.2.1">r-gridextra</requirement> + <requirement type="package" version="3.0">r-ggplot2</requirement> + <requirement type="package" version="2.3">r-gridextra</requirement> </requirements> </xml> |
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| diff -r 17c54820f3be -r 36d38d2cf88c maldi_quant_peakdetection.xml --- a/maldi_quant_peakdetection.xml Thu Oct 25 07:32:17 2018 -0400 +++ b/maldi_quant_peakdetection.xml Fri Feb 15 10:26:45 2019 -0500 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.2">\n+<tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.3">\n <description>\n Peak detection, binning and filtering for mass-spectrometry imaging data\n </description>\n@@ -37,6 +37,7 @@\n \n ## Import imzML file\n coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2]\n+ coordinate_matrix = coordinate_matrix[,c($restriction_conditional.column_x, $restriction_conditional.column_y)]\n \n maldi_data <- importImzMl(\'infile.imzML\',\n coordinates = coordinate_matrix, centroided = $centroids)\n@@ -99,15 +100,16 @@\n cardinal_mzs = Cardinal::mz(msidata)\n maldi_data = list()\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+ 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 }else{\n peaks = list()\n for (spectra in 1:ncol(msidata))\n {\n single_peaks = createMassPeaks(Cardinal::mz(msidata), Cardinal::spectra(msidata)[,spectra], snr=as.numeric(rep("NA", nrow(msidata))))\n peaks[[spectra]] = single_peaks\n- }}\n+ }\n+ coordinates_info = cbind(cardinal_coordinates, c(1:length(peaks)))}\n #end if\n #end if\n \n@@ -125,10 +127,20 @@\n \n ## plot input file spectrum: \n #if $centroids:\n- plot(peaks[[1]], main="First spectrum of input file")\n+ ## Choose random spectra for QC plots\n+ random_spectra = sample(1:length(peaks), 4, replace=FALSE)\n+ par(mfrow = c(2, 2), oma=c(0,0,2,0))\n+ for (random_sample in random_spectra){\n+ plot(peaks[[random_sample]],sub="", main=paste0("spectrum ", random_sample))}\n+ title("Input spectra", outer=TRUE, line=0)\n+\n #else\n- avgSpectra <- averageMassSpectra(maldi_data,method="mean")\n- plot(avgSpectra, main="Average spectrum of input file")\n+ ## Choose random spectra for QC plots\n+ random_spectra = sample(1:length(maldi_data), 4, replace=FALSE)\n+ par(mfrow = c(2, 2), oma=c(0,0,2,0))\n+ for (random_sample in random_spectra){\n+ plot(maldi_data[[random_sample]],sub="", main=paste0("spectrum ", random_sample))}\n+ title("Input spectra", outer=TRUE, line=0)\n #end if\n \n \n@@ -162,10 +174,11 @@\n annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]\n colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"\n \n- ## merge with coordinate information of MSI data\n+ ## merge provided annotation with coordinate information of MSI data\n colnames(coordinates_info)[3] = "pixel_index"\n merged_annotation = merge(coordinates_info, annotation_input, by=c("x", "y"), all.x=TRUE)\n merged_annotation[is.na(merged_annotation)] = "NA"\n+ ## order coordinate information according to pixel index to make sure that the order stays the same\n merged_annotation = merged_annotation[order(merged_annotation\\$pixel_index),]\n samples = as.factor(merged_annotation\\$annotation)\n \n@@ -199,20 +212,28 @@\n maldi_data <- averageMassSpectra(maldi_data, labels=samples,method="mean") ## use average spectra for peak picking\n pixelnames = levels(samples)\n summarized_spectra = TRUE\n-\n+ random_spectra = sample(1:length(maldi_data), 4, replace=TRUE)\n #end if\n \n peaks <- detectPeaks(ma'..b'"file" file="peak_detection4.ibd" name="ibd" compare="sim_size"/>\n+ </output>\n </test>\n </tests>\n <help>\n@@ -596,7 +767,7 @@\n ... \n \n \n-- Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. The file has to contain x values in the first column and y values in the second columns. Further columns are allowed. Tabular files with any header name or no header at all are supported. \n+- Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. Tabular files with any header name or no header at all are supported. \n \n ::\n \n@@ -629,16 +800,21 @@\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+- Monoisotopic peaks: Keeps only the monoisotopic peaks\n \n \n+- Spectra alignment (warping): alignment for (re)calibration of m/z values. \n+\n+ - without external reference m/z: internal reference is obtained by filtering (default 90%) and binning the peaks to find landmark peaks and their average m/z\n+ - with external reference m/z: the m/z provided in a tabular file are used as a reference, at least 10 reference values are recommended\n+ - non linear warping (parametric time warping plus binning) to match the reference peaks (internal or external) to the peaks with the given tolerance. At least two m/z per spectrum are needed for the alignment. This requirement can be skipped by setting "Don\'t throw an error when less than 2 reference m/z were found in a spectrum" to yes. If the not aligned spectra should be set to zero select yes in "If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero". In order to remove such empty spectra set "Should empty spectra be removed" to yes. \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+ 1. Put all m/z 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+ 3. Divide the m/z 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@@ -655,8 +831,8 @@\n \n **Output**\n \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+- centroided, processed imzML file, imzML file is empty when \'Detect peaks on average mass spectra\' is chosen.\n+- pdf with mass spectra plots of four random spectra 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 \n' |
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| diff -r 17c54820f3be -r 36d38d2cf88c test-data/Preprocessing2_QC.pdf |
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| diff -r 17c54820f3be -r 36d38d2cf88c test-data/Preprocessing3_QC.pdf |
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| diff -r 17c54820f3be -r 36d38d2cf88c test-data/align_reference_test2.tabular --- a/test-data/align_reference_test2.tabular Thu Oct 25 07:32:17 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -350 -340 |
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| diff -r 17c54820f3be -r 36d38d2cf88c test-data/inputpeptides.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides.tabular Fri Feb 15 10:26:45 2019 -0500 |
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| @@ -0,0 +1,3 @@ +152 mass1 +328.9 mass2 +185.2 mass3 |
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| diff -r 17c54820f3be -r 36d38d2cf88c test-data/outfile1.ibd |
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| Binary file test-data/outfile1.ibd has changed |
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| diff -r 17c54820f3be -r 36d38d2cf88c test-data/outfile1.imzML --- a/test-data/outfile1.imzML Thu Oct 25 07:32:17 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -imzML file: -total 84 --rw-r--r-- 1 meli meli 67160 Okt 24 10:12 ibd --rw-r--r-- 1 meli meli 15071 Okt 24 10:12 imzml |
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| diff -r 17c54820f3be -r 36d38d2cf88c test-data/outfile1.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outfile1.imzml Fri Feb 15 10:26:45 2019 -0500 |
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| b'@@ -0,0 +1,243 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="out" version="1.1.0">\n+ <cvList count="2">\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.44.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="12:10:2012" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" 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</binaryDataArrayList>\n+ </spectrum>\n+ <spectrum index="5" id="Spectrum=9" defaultArrayLength="1199">\n+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>\n+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>\n+ <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="300.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n+ <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="399.916687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n+ <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>\n+ <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="4.31553230835188"/>\n+ <scanList count="1">\n+ <scan>\n+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>\n+ </scan>\n+ </scanList>\n+ <binaryDataArrayList count="2">\n+ <binaryDataArray encodedLength="0">\n+ <referenceableParamGroupRef ref="mzArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>\n+ <binary/>\n+ </binaryDataArray>\n+ <binaryDataArray encodedLength="0">\n+ <referenceableParamGroupRef ref="intensityArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="57568"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>\n+ <binary/>\n+ </binaryDataArray>\n+ </binaryDataArrayList>\n+ </spectrum>\n+ </spectrumList>\n+ </run>\n+</mzML>\n' |
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| diff -r 17c54820f3be -r 36d38d2cf88c test-data/outfile2.imzML --- a/test-data/outfile2.imzML Thu Oct 25 07:32:17 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -imzML file: -total 276 --rw-r--r-- 1 meli meli 268784 Okt 24 10:12 ibd --rw-r--r-- 1 meli meli 9286 Okt 24 10:12 imzml |
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| diff -r 17c54820f3be -r 36d38d2cf88c test-data/outfile2.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outfile2.imzml Fri Feb 15 10:26:45 2019 -0500 |
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| @@ -0,0 +1,118 @@ +<?xml version="1.0" encoding="utf-8"?> +<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="out" version="1.1.0"> + <cvList count="2"> + <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.44.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/> + <cv id="UO" fullName="Unit Ontology" version="12:10:2012" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/> + <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/> + </cvList> + <fileDescription> + <fileContent> + <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" 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