| Previous changeset 11:f396c176f366 (2020-09-27) Next changeset 13:0852f3d83cc3 (2020-11-29) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0c667acd7cc0d0ef6c4e979ca29372b8c0d92c23" |
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modified:
quality_report.xml test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results2.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results3.pdf test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.pdf test-data/preprocessing_results5.ibd test-data/preprocessing_results5.imzml test-data/preprocessing_results5.imzml.txt test-data/preprocessing_results5.pdf |
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| diff -r f396c176f366 -r ecaebe7c7b54 quality_report.xml --- a/quality_report.xml Sun Sep 27 11:11:53 2020 +0000 +++ b/quality_report.xml Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.0"> +<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.1"> <description> mass spectrometry imaging QC </description> @@ -67,7 +67,6 @@ ###################### calculation of data properties ################################ @DATA_PROPERTIES_INRAM@ - ## Median intensities medint = round(median(int_matrix), digits=2) ## Spectra multiplied with m/z (potential number of peaks) @@ -83,6 +82,8 @@ ## Median and sd # peaks per spectrum medpeaks = round(median(colSums(spectra(msidata)>0, na.rm=TRUE), na.rm=TRUE), digits=0) sdpeaks = round(sd(colSums(spectra(msidata)>0, na.rm=TRUE), na.rm=TRUE), digits=0) +##max window size +max_window = round(mz(msidata)[nrow(msidata)]-mz(msidata)[nrow(msidata)-1], digits=2) ## Processing informations centroidedinfo = centroided(msidata) @@ -138,6 +139,7 @@ "Number of empty spectra", "Median TIC ± sd", "Median # peaks per spectrum ± sd", + "maximum m/z window size", "Centroided", paste0("input m/z (#valid/#input) in \n", "$calibrant_file.display_name")) @@ -146,6 +148,7 @@ paste0(NumemptyTIC), paste0(medTIC, " ± ", sdTIC), paste0(medpeaks, " ± ",sdpeaks), + paste0(max_window), paste0(centroidedinfo), paste0(number_calibrants_valid, " / ", number_calibrants_in)) @@ -222,7 +225,7 @@ pixelxyarray=data.frame(coord(msidata)\$x, coord(msidata)\$y,pixelnumber) colnames(pixelxyarray) = c("x", "y", "pixelnumber") gg_title = "Pixel order" - + print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))+ geom_tile() + coord_fixed()+ ggtitle(gg_title) + theme_bw()+ @@ -755,6 +758,7 @@ if (length(inputcalibrantmasses) != 0){ + ### calculate plusminus values in m/z for each calibrant, this is used for all following plots plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses)) * inputcalibrantmasses @@ -767,6 +771,17 @@ maxmasspixel2 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]+0.5) minmasspixel3 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]-1.5) maxmasspixel3 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]+3) + + ## test if some values are lower than min(mz) + minmasspixel1 = ifelse(length(minmasspixel1)>0, minmasspixel1, 1) + minmasspixel2 = ifelse(length(minmasspixel2)>0, minmasspixel2, 1) + minmasspixel3 = ifelse(length(minmasspixel3)>0, minmasspixel3, 1) + + ## test if min and max are same (more likely for centroided data): + maxmasspixel1 = ifelse(minmasspixel1 != maxmasspixel1, maxmasspixel1, maxmasspixel1 + 1) + maxmasspixel2 = ifelse(minmasspixel2 != maxmasspixel2, maxmasspixel2, maxmasspixel1 + 1) + maxmasspixel3 = ifelse(minmasspixel3 != maxmasspixel3, maxmasspixel3, maxmasspixel1 + 1) + ### find m/z with the highest mean intensity in m/z range (red line in plot 16) and calculate ppm difference for plot 17 filtered_data = msidata_no_NA[mz(msidata_no_NA) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata_no_NA) <= inputcalibrantmasses[mass]+plusminusvalues[mass],] @@ -837,8 +852,10 @@ ### plot the ppm difference calculated above: theor. m/z value to highest m/z value: calibrant_names = as.character(inputcalibrants[,2]) + diff_df = data.frame(differencevector, calibrant_names) + if (sum(is.na(diff_df[,1])) == nrow(diff_df)){ plot(0,type='n',axes=FALSE,ann=FALSE) title(main=paste("plot 17: no peaks in the chosen region, repeat with higher ppm range")) |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results1.ibd |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Sun Sep 27 11:11:53 2020 +0000 +++ b/test-data/preprocessing_results1.imzml Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="25fb4349-d529-4b12-8523-a6aa0306ecf4" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7f41f9f5efcb31248caefc91b7d6edce87d7f42c" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="07177fdd-3760-4df6-8fe2-53d28b280ae8" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="749fe32c8243da06001cf4643c5ce4f1ef5a98a8" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Sun Sep 27 11:11:53 2020 +0000 +++ b/test-data/preprocessing_results1.imzml.txt Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 216 Mai 10 17:37 ibd --rw-r--r-- 1 meli meli 18090 Mai 10 17:37 imzml +-rw-rw-r-- 1 meli meli 216 Oct 5 19:57 ibd +-rw-rw-r-- 1 meli meli 18090 Oct 5 19:57 imzml |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Sun Sep 27 11:11:53 2020 +0000 +++ b/test-data/preprocessing_results2.imzml Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="fa59b434-12e0-47fe-b338-814c92daa7d6" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5764be27b51a23d8c23e4c93befb9d8e57161bd9" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="503079b4-538a-4be6-b70d-e52542c66482" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="a597fe6a0184ef339105b3a932f58726a9af549b" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Sun Sep 27 11:11:53 2020 +0000 +++ b/test-data/preprocessing_results2.imzml.txt Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 64 --rw-r--r-- 1 meli meli 37404 Mai 10 17:38 ibd --rw-r--r-- 1 meli meli 22796 Mai 10 17:38 imzml +-rw-rw-r-- 1 meli meli 37404 Oct 5 19:57 ibd +-rw-rw-r-- 1 meli meli 22796 Oct 5 19:57 imzml |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Sun Sep 27 11:11:53 2020 +0000 +++ b/test-data/preprocessing_results3.imzml Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="d11b7693-3397-4d1f-9e67-29d952701100" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="94906879d47bbdcf97126d50c906dfd76e6681e4" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="be549a7e-87af-4413-9b4c-27221f55ee9a" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4ee7ca6fb3f60e1adbe196068f86bc3209bace58" /> <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Sun Sep 27 11:11:53 2020 +0000 +++ b/test-data/preprocessing_results3.imzml.txt Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 960 Mai 10 17:39 ibd --rw-r--r-- 1 meli meli 18112 Mai 10 17:39 imzml +-rw-rw-r-- 1 meli meli 960 Oct 5 19:58 ibd +-rw-rw-r-- 1 meli meli 18112 Oct 5 19:58 imzml |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Sun Sep 27 11:11:53 2020 +0000 +++ b/test-data/preprocessing_results4.imzml Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9a685278-3bf0-48b5-b7c7-73a7a92625b2" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="036c4b8bf3f2f5a42a223ffd0b895f08b0a65f36" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="48842eaf-40e5-4a3f-831c-2d7a3b7e04b9" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2010ba5b7d44695d891cfe3b6674a5699fa610c0" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results4.imzml.txt --- a/test-data/preprocessing_results4.imzml.txt Sun Sep 27 11:11:53 2020 +0000 +++ b/test-data/preprocessing_results4.imzml.txt Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 84 --rw-rw-r-- 1 meli meli 62696 Sep 20 11:48 ibd --rw-rw-r-- 1 meli meli 18199 Sep 20 11:48 imzml +-rw-rw-r-- 1 meli meli 62696 Oct 5 19:58 ibd +-rw-rw-r-- 1 meli meli 18199 Oct 5 19:58 imzml |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results5.imzml --- a/test-data/preprocessing_results5.imzml Sun Sep 27 11:11:53 2020 +0000 +++ b/test-data/preprocessing_results5.imzml Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="3aff713c-00ec-422d-b63d-efd45fbdd7cc" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9316138c1e7484662943bb206c79c2d074121530" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="56965a72-6fd7-4879-bb80-b72cb3af4a62" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5e07e272de044937cd6be7bfdbf2f4730aad10a9" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r f396c176f366 -r ecaebe7c7b54 test-data/preprocessing_results5.imzml.txt --- a/test-data/preprocessing_results5.imzml.txt Sun Sep 27 11:11:53 2020 +0000 +++ b/test-data/preprocessing_results5.imzml.txt Tue Oct 06 08:16:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 428 --rw-r--r-- 1 meli meli 415936 Mai 10 17:40 ibd --rw-r--r-- 1 meli meli 18569 Mai 10 17:40 imzml +-rw-rw-r-- 1 meli meli 415936 Oct 5 19:59 ibd +-rw-rw-r-- 1 meli meli 18569 Oct 5 19:59 imzml |
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