| Previous changeset 2:3642ed221eb2 (2019-02-15) Next changeset 4:9b6b86e771c2 (2019-03-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 |
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modified:
spectra_plots.xml 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.RData test-data/preprocessing_results5.pdf |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 spectra_plots.xml --- a/spectra_plots.xml Fri Feb 15 10:23:28 2019 -0500 +++ b/spectra_plots.xml Thu Feb 28 09:27:53 2019 -0500 |
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| @@ -56,7 +56,7 @@ #if str($processed_cond.processed_file) == "processed": ##processed file needs to be converted into matrix to be able to replace NAs iData(msidata) <- iData(msidata)[] - spectra(msidata)[][is.na(spectra(msidata)[])] = 0 + spectra(msidata)[is.na(spectra(msidata))] = 0 #else spectra(msidata)[is.na(spectra(msidata))] = 0 #end if @@ -101,7 +101,7 @@ ##################### III) plot full mass spectrum ################# - plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy)) + plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy), main="Mass spectrum of full m/z range") ##################### IV) plot zoom-in mass spectrum ############### @@ -199,9 +199,9 @@ key_legend = TRUE }else{key_legend = FALSE} - plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE) + plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE, main="Average mass spectrum of full m/z range") }else{ - plot(msidata, pixel=1:ncol(msidata), key=TRUE)} + plot(msidata, pixel=1:ncol(msidata), key=TRUE, main="Average mass spectrum of full m/z range")} ##################### II) Sample: plot zoom-in mass spectrum ########## |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results1.ibd |
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| Binary file test-data/preprocessing_results1.ibd has changed |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Fri Feb 15 10:23:28 2019 -0500 +++ b/test-data/preprocessing_results1.imzml Thu Feb 28 09:27:53 2019 -0500 |
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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="{002DF5BA-0549-44DF-A8BB-27DA3E197EB7}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0379019A6F9D0B55F9217420030633F7163AF9D3" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{728FBFFE-E6FC-4283-8068-393A66F6BD5C}" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="375094460F3B80674CB2F541DCD9928B3D61B2FF" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Fri Feb 15 10:23:28 2019 -0500 +++ b/test-data/preprocessing_results1.imzml.txt Thu Feb 28 09:27:53 2019 -0500 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 96 Feb 12 21:24 ibd --rw-r--r-- 1 meli meli 16714 Feb 12 21:24 imzml +-rw-r--r-- 1 meli meli 96 Feb 24 14:11 ibd +-rw-r--r-- 1 meli meli 16714 Feb 24 14:11 imzml |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results1.pdf |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results2.ibd |
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| Binary file test-data/preprocessing_results2.ibd has changed |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Fri Feb 15 10:23:28 2019 -0500 +++ b/test-data/preprocessing_results2.imzml Thu Feb 28 09:27:53 2019 -0500 |
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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="{84BEACDD-B841-4730-81A0-A19A28C7B48A}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1BC49DCCC566E7A6938CE3DE62090650C2A04798" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{40F230A1-1893-4A8C-BAE2-A8BBEF24DB20}" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="417ADF38FBC4D0304A9B75B4C85799137846DD2F" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Fri Feb 15 10:23:28 2019 -0500 +++ b/test-data/preprocessing_results2.imzml.txt Thu Feb 28 09:27:53 2019 -0500 |
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| @@ -1,4 +1,4 @@ imzML file: total 80 --rw-r--r-- 1 meli meli 54720 Feb 12 21:25 ibd --rw-r--r-- 1 meli meli 21132 Feb 12 21:25 imzml +-rw-r--r-- 1 meli meli 54720 Feb 24 14:12 ibd +-rw-r--r-- 1 meli meli 21132 Feb 24 14:12 imzml |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results2.pdf |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results3.ibd |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Fri Feb 15 10:23:28 2019 -0500 +++ b/test-data/preprocessing_results3.imzml Thu Feb 28 09:27:53 2019 -0500 |
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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="{4C387879-DE12-49A4-878F-6980D6F7C6F0}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="94ED775BCF16644D23DACFCA1E62D28D5C755178" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{D767424F-5E74-45AB-AF1B-0D25244B435B}" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="445E32981D0B3D08ED2BA74E11500A3A08CDB9B7" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Fri Feb 15 10:23:28 2019 -0500 +++ b/test-data/preprocessing_results3.imzml.txt Thu Feb 28 09:27:53 2019 -0500 |
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| @@ -1,4 +1,4 @@ imzML file: total 36 --rw-r--r-- 1 meli meli 14216 Feb 12 21:26 ibd --rw-r--r-- 1 meli meli 16824 Feb 12 21:26 imzml +-rw-r--r-- 1 meli meli 14216 Feb 24 14:12 ibd +-rw-r--r-- 1 meli meli 16824 Feb 24 14:12 imzml |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Fri Feb 15 10:23:28 2019 -0500 +++ b/test-data/preprocessing_results4.imzml Thu Feb 28 09:27:53 2019 -0500 |
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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="{26018306-9D72-49F5-89CB-68E4DDE0527C}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="BA6411EC5A5A59ABE5BD7005F4ED8FCEBA775A8E" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{FE932E04-42E4-4D89-B721-2A6CE83250B6}" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="36C7C916C176DD85CBBF4B7FA969C92B9403768D" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results4.imzml.txt --- a/test-data/preprocessing_results4.imzml.txt Fri Feb 15 10:23:28 2019 -0500 +++ b/test-data/preprocessing_results4.imzml.txt Thu Feb 28 09:27:53 2019 -0500 |
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| @@ -1,4 +1,4 @@ imzML file: total 28 --rw-r--r-- 1 meli meli 6376 Feb 12 21:29 ibd --rw-r--r-- 1 meli meli 16801 Feb 12 21:29 imzml +-rw-r--r-- 1 meli meli 6376 Feb 24 14:13 ibd +-rw-r--r-- 1 meli meli 16801 Feb 24 14:13 imzml |
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