| Previous changeset 6:d286ff4600dd (2020-04-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc |
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modified:
maldi_macros.xml maldi_quant_peakdetection.xml test-data/masspeaks3.tabular test-data/masspeaks4.tabular 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/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/Example_Processed.ibd test-data/Example_Processed.imzML test-data/annotations.tabular test-data/int3.tabular test-data/int4.tabular test-data/masspeaks5.tabular test-data/peak_detection3.imzml.txt.html test-data/peak_detection5.ibd test-data/peak_detection5.imzml test-data/peak_detection5.imzml.txt test-data/peakdetection5_QC.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzML |
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removed:
test-data/annotations_output3.tabular test-data/msidata_1.RData test-data/testfile_squares.rdata |
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| diff -r d286ff4600dd -r 160538a890a6 maldi_macros.xml --- a/maldi_macros.xml Thu Apr 16 17:53:18 2020 -0400 +++ b/maldi_macros.xml Sat Mar 04 19:14:04 2023 +0000 |
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| @@ -1,6 +1,5 @@ <macros> <token name="@R_IMPORTS@"><![CDATA[ - library (Cardinal) library (MALDIquantForeign) library (MALDIquant) library (ggplot2) @@ -14,15 +13,14 @@ ]]> </token> - <token name="@VERSION@">1.18.0</token> + <token name="@VERSION@">1.22.0</token> <xml name="requirements"> <requirements> - <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="3.0">r-ggplot2</requirement> + <requirement type="package" version="4.2.2">r-base</requirement> + <requirement type="package" version="0.13">r-maldiquantforeign</requirement> + <requirement type="package" version="1.22">r-maldiquant</requirement> + <requirement type="package" version="3.4.1">r-ggplot2</requirement> <requirement type="package" version="2.3">r-gridextra</requirement> </requirements> </xml> @@ -31,6 +29,7 @@ <citations> <citation type="doi">10.1093/bioinformatics/bts447</citation> <citation type="doi">10.1007/978-3-319-45809-0_6</citation> + <citation type="doi">10.1093/gigascience/giz143</citation> </citations> </xml> </macros> |
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| diff -r d286ff4600dd -r 160538a890a6 maldi_quant_peakdetection.xml --- a/maldi_quant_peakdetection.xml Thu Apr 16 17:53:18 2020 -0400 +++ b/maldi_quant_peakdetection.xml Sat Mar 04 19:14:04 2023 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.6">\n+<tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.0">\n <description>\n Peak detection, binning and filtering for mass-spectrometry imaging data\n </description>\n@@ -15,8 +15,6 @@\n cp \'${infile.extra_files_path}/hdr\' infile.hdr &&\n cp \'${infile.extra_files_path}/img\' infile.img &&\n cp \'${infile.extra_files_path}/t2m\' infile.t2m &&\n- #else\n- ln -s \'$infile\' infile.RData &&\n #end if\n cat \'${maldi_quant_peak_detection}\' &&\n Rscript \'${maldi_quant_peak_detection}\' &&\n@@ -36,14 +34,18 @@\n \n print(\'Reading mask region\')\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 = $centroids)\n- pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")\n-\n+\t\t## Import imzML file\n+\t\tcoordinate_matrix = read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE)\n+\t\tcoordinate_matrix = coordinate_matrix[,c($restriction_conditional.column_x, $restriction_conditional.column_y)]\n+\t\t#if str($centroids) == "TRUE"\n+\t\t peaks <- importImzMl(\'infile.imzML\',\n+\t\t coordinates = as.matrix(coordinate_matrix), centroided = $centroids) \n+\t\t\tpixelnames = paste("xy", coordinates(peaks)[,1],coordinates(peaks)[,2], sep="_") \n+\t\t#else\n+\t\t\tmaldi_data <- importImzMl(\'infile.imzML\',\n+\t\t coordinates = as.matrix(coordinate_matrix), centroided = $centroids) \n+\t\t\tpixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")\n+\t\t#end if\n \n #else:\n \n@@ -77,40 +79,6 @@\n peaks[[spectra]] = single_peaks\n }\n \n- #else\n- print(\'rdata file\')\n- loadRData <- function(fileName){\n- #loads an RData file, and returns it\n- load(fileName)\n- get(ls()[ls() != "fileName"])\n- }\n- msidata = loadRData(\'infile.RData\')\n- centroided(msidata) = $centroids\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- if (centroided(msidata) == FALSE){\n- ## create mass spectrum object\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- }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- coordinates_info = cbind(cardinal_coordinates, c(1:length(peaks)))}\n #end if\n #end if\n \n@@ -129,8 +97,7 @@\n ## plot input file spectrum: \n #if $centroids:\n ## Choose random spectra for QC plots\n- print(length(peaks))\n- '..b'name="method" value="Filtering"/>\n- <param name="minFrequency" value="0.5"/>\n- <param name="minNumber" value="3"/>\n- <param name="filter_annot_groups" value="TRUE"/>\n- <param name="mergeWhitelists" value="FALSE"/>\n- </conditional>\n- </repeat>\n- <output name="plots" file="peakdetection3_QC.pdf" compare="sim_size"/>\n- <output name="intensity_matrix" file="intensity_matrix3.tabular"/>\n- <output name="masspeaks" file="masspeaks3.tabular"/>\n- <output name="outfile_imzml" ftype="imzml" file="peak_detection3.imzml.txt" lines_diff="4">\n- <extra_files type="file" file="peak_detection3.imzml" name="imzml" lines_diff="6"/>\n- <extra_files type="file" file="peak_detection3.ibd" name="ibd" compare="sim_size"/>\n- </output>\n- </test>\n- <test>\n- <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>\n- <param name="method" value="Peak_detection"/>\n- <param name="peak_method" value="MAD"/>\n- <param name="halfWindowSize" value="20"/>\n- <param name="snr" value="2"/>\n <output name="plots" file="peakdetection4_QC.pdf" compare="sim_size"/>\n- <output name="intensity_matrix" file="intensity_matrix4.tabular"/>\n+ <output name="intensity_matrix" file="int4.tabular"/>\n <output name="masspeaks" file="masspeaks4.tabular"/>\n <output name="outfile_imzml" ftype="imzml" file="peak_detection4.imzml.txt" lines_diff="4">\n <extra_files type="file" file="peak_detection4.imzml" name="imzml" lines_diff="6"/>\n <extra_files type="file" file="peak_detection4.ibd" name="ibd" compare="sim_size"/>\n </output>\n </test>\n+ <test>\n+ <param name="infile" value="" ftype="imzml">\n+ <composite_data value="preprocessing_results3.imzML"/>\n+ <composite_data value="preprocessing_results3.ibd"/>\n+ </param>\n+ <param name="centroids" value="TRUE"/>\n+ <conditional name="restriction_conditional">\n+\t\t <param name="restriction" value="restrict"/>\n+ <param name="coordinates_file" value="annotations.tabular"/>\n+ <param name="column_x" value="1"/>\n+ <param name="column_y" value="2"/>\n+ <param name="coordinates_header" value="TRUE"/>\n+ </conditional>\n+ <repeat name="methods">\n+ <conditional name="methods_conditional">\n+ <param name="method" value="skip_preprocessing"/>\n+ </conditional>\n+ </repeat>\n+ <output name="plots" file="peakdetection5_QC.pdf" compare="sim_size"/>\n+ <output name="masspeaks" file="masspeaks5.tabular"/>\n+ <output name="outfile_imzml" ftype="imzml" file="peak_detection5.imzml.txt" lines_diff="4">\n+ <extra_files type="file" file="peak_detection5.imzml" name="imzml" lines_diff="6"/>\n+ <extra_files type="file" file="peak_detection5.ibd" name="ibd" compare="sim_size"/>\n+ </output>\n+ </test>\n </tests>\n+ \n <help>\n <![CDATA[\n \n@@ -824,8 +860,7 @@\n \n - MSI data: 3 types of input data can be used:\n \n- - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_\n- - Cardinal "MSImageSet" data saved as .RData\n+ - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/imzml/>`_\n - MSI data as peak list (tabular file) with the columns named "snr", "mass", "intensity" and "spectrum". The spectrum has to be in the following format: xy_1_1 (for pixel coordinates x1y1). The header must have exactly the four column names.\n \n :: \n' |
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| diff -r d286ff4600dd -r 160538a890a6 test-data/Example_Processed.ibd |
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| Binary file test-data/Example_Processed.ibd has changed |
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| diff -r d286ff4600dd -r 160538a890a6 test-data/Example_Processed.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Example_Processed.imzML Sat Mar 04 19:14:04 2023 +0000 |
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| b'@@ -0,0 +1,380 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<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" xmlns="http://psi.hupo.org/ms/mzml" version="1.1">\n+ <cvList count="4">\n+ <cv URI="http://ontologies.berkeleybop.org/pato.obo" fullName="Phenotype And Trait Ontology" id="PATO" version="releases/2017-07-10"/>\n+ <cv URI="http://ontologies.berkeleybop.org/uo.obo" fullName="Units of Measurement Ontology" id="UO" version="releases/2017-09-25"/>\n+ <cv URI="https://raw.githubusercontent.com/hupo-psi/psi-ms-cv/master/psi-ms.obo" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" id="MS" version="4.1.0"/>\n+ <cv URI="https://raw.githubusercontent.com/imzML/imzML/master/imagingMS.obo" fullName="Mass Spectrometry Imaging Ontology" id="IMS" version="1.1.0"/>\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>\n+ <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9d501bdc53444916b7e97e795b02c856"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7e8fdb93053915d3edb51b70aa0619ac209964df"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>\n+ </fileContent>\n+ <sourceFileList count="1">\n+ <sourceFile id="sf1" location="C:\\Users\\Thorsten Schramm\\Documents\\Promotion\\imzML\\Website\\files\\Beispiel-Dateien\\Example images\\" name="Example.raw">\n+ <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format"/>\n+ <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>\n+ </sourceFile>\n+ </sourceFileList>\n+ <contact>\n+ <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>\n+ <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Institut f\xfcr Anorganische und Analytische Chemie"/>\n+ <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstra\xdfe 60, Haus 16, Gie\xdfen, Germany"/>\n+ <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>\n+ </contact>\n+ </fileDescription>\n+ <referenceableParamGroupList count="4">\n+ <referenceableParamGroup id="mzArray">\n+ <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>\n+ <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\n+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>\n+ </referenceableParamGroup>\n+ <referenceableParamGroup id="intensityArray">\n+ <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>\n+ <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\n+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>\n+ </referenceableParamGroup>\n+ <referenceableParamGroup id="scan1">\n+ <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan"/>\n+ <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - 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| diff -r d286ff4600dd -r 160538a890a6 test-data/annotations.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations.tabular Sat Mar 04 19:14:04 2023 +0000 |
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| @@ -0,0 +1,4 @@ +x y pixel_index annotation +3 1 3 col3 +2 2 5 col2 +1 3 7 col1 |
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| diff -r d286ff4600dd -r 160538a890a6 test-data/annotations_output3.tabular --- a/test-data/annotations_output3.tabular Thu Apr 16 17:53:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -x y pixel_index annotation -3 1 3 col3 -2 2 5 col2 -1 3 7 col1 |
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| diff -r d286ff4600dd -r 160538a890a6 test-data/int3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int3.tabular Sat Mar 04 19:14:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,102 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|
| b |
| diff -r d286ff4600dd -r 160538a890a6 test-data/int4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int4.tabular Sat Mar 04 19:14:04 2023 +0000 |
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|
| b |
| diff -r d286ff4600dd -r 160538a890a6 test-data/masspeaks3.tabular --- a/test-data/masspeaks3.tabular Thu Apr 16 17:53:18 2020 -0400 +++ b/test-data/masspeaks3.tabular Sat Mar 04 19:14:04 2023 +0000 |
| b |
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|
| b |
| diff -r d286ff4600dd -r 160538a890a6 test-data/masspeaks4.tabular --- a/test-data/masspeaks4.tabular Thu Apr 16 17:53:18 2020 -0400 +++ b/test-data/masspeaks4.tabular Sat Mar 04 19:14:04 2023 +0000 |
| b |
| b'@@ -1,1862 +1,1083 @@\n 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|
| b |
| diff -r d286ff4600dd -r 160538a890a6 test-data/masspeaks5.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masspeaks5.tabular Sat Mar 04 19:14:04 2023 +0000 |
| b |
| @@ -0,0 +1,109 @@ +snr mass intensity spectrum +NA 1199.57592773438 3.40581107139587 xy_3_1 +NA 1200.57067871094 1.98672306537628 xy_3_1 +NA 1201.54187011719 0 xy_3_1 +NA 1208.521484375 2.55435824394226 xy_3_1 +NA 1209.54284667969 2.36514663696289 xy_3_1 +NA 1210.51892089844 0 xy_3_1 +NA 1214.50366210938 0 xy_3_1 +NA 1220.48840332031 0 xy_3_1 +NA 1221.57312011719 0 xy_3_1 +NA 1223.47229003906 2.27054071426392 xy_3_1 +NA 1224.49499511719 2.17593479156494 xy_3_1 +NA 1225.49890136719 0 xy_3_1 +NA 1240.46606445312 2.45975232124329 xy_3_1 +NA 1244.46423339844 0 xy_3_1 +NA 1245.45471191406 0 xy_3_1 +NA 1261.51550292969 0 xy_3_1 +NA 1264.39379882812 3.12199330329895 xy_3_1 +NA 1264.55151367188 0 xy_3_1 +NA 1265.37878417969 2.55435824394226 xy_3_1 +NA 1266.5478515625 2.27054071426392 xy_3_1 +NA 1267.52416992188 3.97344613075256 xy_3_1 +NA 1268.54431152344 2.64896416664124 xy_3_1 +NA 1281.48413085938 0 xy_3_1 +NA 1282.44689941406 2.17593479156494 xy_3_1 +NA 1287.41162109375 0 xy_3_1 +NA 1289.49475097656 2.64896416664124 xy_3_1 +NA 1290.46948242188 0 xy_3_1 +NA 1296.54089355469 1.98672306537628 xy_3_1 +NA 1297.56005859375 2.17593479156494 xy_3_1 +NA 1298.53125 0 xy_3_1 +NA 1314.54272460938 0 xy_3_1 +NA 1332.51330566406 0 xy_3_1 +NA 1333.48498535156 0 xy_3_1 +NA 1347.60522460938 0 xy_3_1 +NA 1348.55407714844 0 xy_3_1 +NA 1354.47863769531 2.17593479156494 xy_3_1 +NA 1199.57592773438 0 xy_2_2 +NA 1200.57067871094 0 xy_2_2 +NA 1201.54187011719 0 xy_2_2 +NA 1208.521484375 0 xy_2_2 +NA 1209.54284667969 0 xy_2_2 +NA 1210.51892089844 2.13411235809326 xy_2_2 +NA 1214.50366210938 0 xy_2_2 +NA 1220.48840332031 0 xy_2_2 +NA 1221.57312011719 0 xy_2_2 +NA 1223.47229003906 0 xy_2_2 +NA 1224.49499511719 0 xy_2_2 +NA 1225.49890136719 0 xy_2_2 +NA 1240.46606445312 0 xy_2_2 +NA 1244.46423339844 0 xy_2_2 +NA 1245.45471191406 0 xy_2_2 +NA 1261.51550292969 0 xy_2_2 +NA 1264.39379882812 2.25267434120178 xy_2_2 +NA 1264.55151367188 0 xy_2_2 +NA 1265.37878417969 0 xy_2_2 +NA 1266.5478515625 0 xy_2_2 +NA 1267.52416992188 2.48979783058167 xy_2_2 +NA 1268.54431152344 0 xy_2_2 +NA 1281.48413085938 0 xy_2_2 +NA 1282.44689941406 0 xy_2_2 +NA 1287.41162109375 0 xy_2_2 +NA 1289.49475097656 2.13411235809326 xy_2_2 +NA 1290.46948242188 0 xy_2_2 +NA 1296.54089355469 0 xy_2_2 +NA 1297.56005859375 0 xy_2_2 +NA 1298.53125 0 xy_2_2 +NA 1314.54272460938 0 xy_2_2 +NA 1332.51330566406 0 xy_2_2 +NA 1333.48498535156 0 xy_2_2 +NA 1347.60522460938 0 xy_2_2 +NA 1348.55407714844 0 xy_2_2 +NA 1354.47863769531 0 xy_2_2 +NA 1199.57592773438 6.61364221572876 xy_1_3 +NA 1200.57067871094 3.77922415733337 xy_1_3 +NA 1201.54187011719 2.28328132629395 xy_1_3 +NA 1208.521484375 0 xy_1_3 +NA 1209.54284667969 0 xy_1_3 +NA 1210.51892089844 0 xy_1_3 +NA 1214.50366210938 2.36201500892639 xy_1_3 +NA 1220.48840332031 2.36201500892639 xy_1_3 +NA 1221.57312011719 2.04707980155945 xy_1_3 +NA 1223.47229003906 0 xy_1_3 +NA 1224.49499511719 0 xy_1_3 +NA 1225.49890136719 1.96834588050842 xy_1_3 +NA 1240.46606445312 0 xy_1_3 +NA 1244.46423339844 0 xy_1_3 +NA 1245.45471191406 0 xy_1_3 +NA 1261.51550292969 0 xy_1_3 +NA 1264.39379882812 0 xy_1_3 +NA 1264.55151367188 0 xy_1_3 +NA 1265.37878417969 0 xy_1_3 +NA 1266.5478515625 0 xy_1_3 +NA 1267.52416992188 2.12581348419189 xy_1_3 +NA 1268.54431152344 2.12581348419189 xy_1_3 +NA 1281.48413085938 0 xy_1_3 +NA 1282.44689941406 0 xy_1_3 +NA 1287.41162109375 0 xy_1_3 +NA 1289.49475097656 1.96834588050842 xy_1_3 +NA 1290.46948242188 0 xy_1_3 +NA 1296.54089355469 2.75568413734436 xy_1_3 +NA 1297.56005859375 2.59821653366089 xy_1_3 +NA 1298.53125 2.04707980155945 xy_1_3 +NA 1314.54272460938 0 xy_1_3 +NA 1332.51330566406 1.96834588050842 xy_1_3 +NA 1333.48498535156 0 xy_1_3 +NA 1347.60522460938 2.20454740524292 xy_1_3 +NA 1348.55407714844 2.20454740524292 xy_1_3 +NA 1354.47863769531 2.04707980155945 xy_1_3 |
| b |
| diff -r d286ff4600dd -r 160538a890a6 test-data/msidata_1.RData |
| b |
| Binary file test-data/msidata_1.RData has changed |
| b |
| diff -r d286ff4600dd -r 160538a890a6 test-data/peak_detection2.ibd |
| b |
| Binary file test-data/peak_detection2.ibd has changed |
| b |
| diff -r d286ff4600dd -r 160538a890a6 test-data/peak_detection2.imzml --- a/test-data/peak_detection2.imzml Thu Apr 16 17:53:18 2020 -0400 +++ b/test-data/peak_detection2.imzml Sat Mar 04 19:14:04 2023 +0000 |
| b |
| @@ -8,14 +8,14 @@ <fileDescription> <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{cc20fc46-860b-42cc-91a3-69e42329f338}"/> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="64664d4479a6efec0398b19c652ffa2688d95d92"/> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{9e610205-f935-4163-85d0-b1cb4001c0d8}"/> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="917d862c478f33cd1fcc8a43ad01f226338dd4df"/> <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/> <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/> </fileContent> </fileDescription> <softwareList count="1"> - <software id="MALDIquantForeign" version="0.11.5"/> + <software id="MALDIquantForeign" version="0.13"/> </softwareList> <referenceableParamGroupList count="2"> <referenceableParamGroup id="mzArray"> |
| b |
| diff -r d286ff4600dd -r 160538a890a6 test-data/peak_detection2.imzml.txt --- a/test-data/peak_detection2.imzml.txt Thu Apr 16 17:53:18 2020 -0400 +++ b/test-data/peak_detection2.imzml.txt Sat Mar 04 19:14:04 2023 +0000 |
| b |
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