| Previous changeset 9:ca727a6dede6 (2020-09-24) Next changeset 11:e86a8be551b9 (2020-10-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" |
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modified:
macros.xml preprocessing.xml test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/analyze75_filtered2.pdf test-data/imzml_filtered3.pdf test-data/imzml_filtered4.pdf test-data/imzml_filtered5.pdf test-data/imzml_filtered8.pdf test-data/out3.ibd test-data/out3.imzml test-data/out3.imzml.txt test-data/out4.ibd test-data/out4.imzml test-data/out4.imzml.txt test-data/out5.ibd test-data/out5.imzml test-data/out5.imzml.txt test-data/out6.ibd test-data/out6.imzml test-data/out6.imzml.txt test-data/out7.ibd test-data/out7.imzml test-data/out7.imzml.txt test-data/out8.ibd test-data/out8.imzml test-data/out8.imzml.txt test-data/rdata_notfiltered.pdf |
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| diff -r ca727a6dede6 -r 5abc3ab4792c macros.xml --- a/macros.xml Thu Sep 24 11:43:31 2020 +0000 +++ b/macros.xml Sun Sep 27 11:10:30 2020 +0000 |
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| @@ -117,6 +117,13 @@ <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ ########################### QC numbers ######################## ## including intensity calculations which need data in RAM + + int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use + ## Number of NA in spectra matrix + NAcount = sum(is.na(int_matrix)) + ## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata + int_matrix[is.na(int_matrix)] <- 0 + ## Number of features (mz) maxfeatures = length(features(msidata)) ## Range mz @@ -131,14 +138,12 @@ minimumy = min(coord(msidata)[,2]) maximumy = max(coord(msidata)[,2]) ## Range of intensities - minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) - maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) + minint = round(min(int_matrix), digits=2) + maxint = round(max(int_matrix), digits=2) ## Number of intensities > 0, for if conditions - npeaks= sum(as.matrix(spectra(msidata))>0, na.rm=TRUE) + npeaks= sum(int_matrix>0) ## Number of NA in spectra matrix - NAcount = sum(is.na(spectra(msidata))) - ## Number of NA in spectra matrix - infcount = sum(is.infinite(as.matrix(spectra(msidata)))) + infcount = sum(is.infinite(int_matrix)) ## Number of duplicated coordinates dupl_coord = sum(duplicated(coord(msidata))) properties = c("Number of m/z features", |
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| diff -r ca727a6dede6 -r 5abc3ab4792c preprocessing.xml --- a/preprocessing.xml Thu Sep 24 11:43:31 2020 +0000 +++ b/preprocessing.xml Sun Sep 27 11:10:30 2020 +0000 |
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| b'@@ -74,7 +74,7 @@\n ## Choose random spectra for QC plots\n random_spectra = sample(pixels(msidata), 4, replace=FALSE)\n par(oma=c(0,0,2,0))\n- print(plot(msidata, pixel=random_spectra))\n+ print(plot(msidata, pixel=random_spectra, col="black"))\n title("Input spectra", outer=TRUE, line=0)\n \n ############################### Preprocessing steps ###########################\n@@ -88,10 +88,6 @@\n print(\'Normalization\')\n ##normalization\n \n- if (class(msidata) == "MSProcessedImagingExperiment"){\n- msidata = as(msidata, "MSContinuousImagingExperiment")\n- }\n-\n msidata = normalize(msidata, method="$method.methods_conditional.methods_for_normalization.normalization_method")\n msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))\n \n@@ -105,7 +101,7 @@\n normalized = c(minmz, maxmz,maxfeatures, pixelcount)\n QC_numbers= cbind(QC_numbers, normalized)\n vectorofactions = append(vectorofactions, "normalized")\n- print(plot(msidata, pixel=random_spectra))\n+ print(plot(msidata, pixel=random_spectra, col="black"))\n title("Spectra after normalization", outer=TRUE, line=0)\n \n ############################### Baseline reduction ###########################\n@@ -114,10 +110,6 @@\n print(\'Baseline_reduction\')\n ##baseline reduction\n \n- if (class(msidata) == "MSProcessedImagingExperiment"){\n- msidata = as(msidata, "MSContinuousImagingExperiment")\n- }\n-\n msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline, spar=$method.methods_conditional.spar_baseline)\n msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))\n \n@@ -130,7 +122,7 @@\n baseline = c(minmz, maxmz,maxfeatures, pixelcount)\n QC_numbers= cbind(QC_numbers, baseline)\n vectorofactions = append(vectorofactions, "baseline red.")\n- print(plot(msidata, pixel=random_spectra))\n+ print(plot(msidata, pixel=random_spectra, col="black"))\n title("Spectra after baseline reduction", outer=TRUE, line=0)\n \n ############################### Smoothing ###########################\n@@ -139,11 +131,6 @@\n print(\'Smoothing\')\n ## Smoothing\n \n- if (class(msidata) == "MSProcessedImagingExperiment"){\n- msidata = as(msidata, "MSContinuousImagingExperiment")\n- }\n-\n-\n #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == \'gaussian\':\n print(\'gaussian smoothing\')\n \n@@ -176,7 +163,7 @@\n smoothed = c(minmz, maxmz,maxfeatures, pixelcount)\n QC_numbers= cbind(QC_numbers, smoothed)\n vectorofactions = append(vectorofactions, "smoothed")\n- print(plot(msidata, pixel=random_spectra))\n+ print(plot(msidata, pixel=random_spectra, col="black"))\n title("Spectra after smoothing", outer=TRUE, line=0)\n \n \n@@ -211,7 +198,7 @@\n mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount)\n QC_numbers= cbind(QC_numbers, mz_aligned)\n vectorofactions = append(vectorofactions, "mz aligned")\n- print(plot(msidata, pixel=random_spectra))\n+ print(plot(msidata, pixel=random_spectra, col="black"))\n title("Spectra after m/z alignment", outer=TRUE, line=0)\n \n \n@@ -240,10 +227,6 @@\n #end if\n msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))\n \n- #if str($method.methods_conditional.imzml_output) == "cont_format":\n- #set $continuous_format = True\n- #end if\n-\n \n ############################### QC ###########################\n \n@@ -254,7 +237,7 @@\n picked = c(minmz, maxmz,maxfeatures, pixelcount)\n QC_number'..b' $continuous_format = True\n+ #end if\n \n if (nrow(msidata) > 0){\n ## make sure that coordinates are integers\n@@ -578,7 +562,6 @@\n <when value="mad"/>\n <when value="simple"/>\n </conditional>\n- <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/>\n </when>\n <when value="Peak_alignment">\n <param name="value_diffalignment" type="float" value="200"\n@@ -597,7 +580,6 @@\n <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/>\n </when>\n </conditional>\n- <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format" help= "Processed imzML works only in MALDIquant tools, not yet in MSI tools (Cardinal)"/>\n </when>\n <when value="Peak_filtering">\n <param name="frequ_filtering" type="float" value="0.01" max="1" min="0" label="Minimum frequency" help="Peaks that occur in the dataset in lesser proportion than this will be dropped (0.01 --> filtering for 1% of spectra)"/>\n@@ -661,6 +643,7 @@\n </when>\n </conditional>\n </repeat>\n+ <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/>\n </inputs>\n <outputs>\n <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>\n@@ -696,13 +679,11 @@\n <param name="blocks_picking" value="3"/>\n <param name="window_picking" value="3"/>\n <param name="SNR_picking_method" value="3"/>\n- <param name="imzml_output" value="cont_format"/>\n </conditional>\n </repeat>\n <repeat name="methods">\n <conditional name="methods_conditional">\n <param name="preprocessing_method" value="Peak_alignment"/>\n- <param name="imzml_output" value="cont_format"/>\n </conditional>\n </repeat>\n <repeat name="methods">\n@@ -719,6 +700,7 @@\n </conditional>\n </conditional>\n </repeat>\n+ <param name="imzml_output" value="cont_format"/>\n <output name="QC_overview" file="preprocessing_results1.pdf" compare="sim_size"/>\n <output name="outfile_imzml" ftype="imzml" file="preprocessing_results1.imzml.txt" compare="sim_size">\n <extra_files type="file" file="preprocessing_results1.imzml" name="imzml" lines_diff="6"/>\n@@ -736,15 +718,14 @@\n <conditional name="methods_for_picking">\n <param name="picking_method" value="adaptive"/>\n </conditional>\n- <param name="imzml_output" value="cont_format"/>\n </conditional>\n </repeat>\n <repeat name="methods">\n <conditional name="methods_conditional">\n <param name="preprocessing_method" value="Peak_alignment"/>\n- <param name="imzml_output" value="cont_format"/>\n </conditional>\n </repeat>\n+ <param name="imzml_output" value="cont_format"/>\n <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/>\n <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size">\n <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/>\n' |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/analyze75_filtered2.pdf |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out3.imzml --- a/test-data/out3.imzml Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out3.imzml Sun Sep 27 11:10:30 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="c6cc990a-d910-4c17-aedd-ceb204b4d105" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ef8c4f864d0386736c986ebb4d4eb29a726e42d4" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="97f42eea-750c-49e4-b46d-08c548dc3b9d" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4e046226f81e9c78255df625ca3546ef26dd0693" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out3.imzml.txt --- a/test-data/out3.imzml.txt Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out3.imzml.txt Sun Sep 27 11:10:30 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-rw-r-- 1 meli meli 9616 Aug 23 17:39 ibd --rw-rw-r-- 1 meli meli 8958 Aug 23 17:39 imzml +-rw-rw-r-- 1 meli meli 9616 Sep 27 10:51 ibd +-rw-rw-r-- 1 meli meli 8958 Sep 27 10:51 imzml |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out4.ibd |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out4.imzml --- a/test-data/out4.imzml Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out4.imzml Sun Sep 27 11:10:30 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="78fa5a7c-8dc8-4ff1-ad77-b19714f285cb" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="64d40f8c65af1399e24d94569f4dd3fdbf43a901" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="37f3f75a-82c4-47c5-b78e-28fb8697e59b" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1746fd2ec8a12707330a78ff5a0ff98cb53dca42" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out4.imzml.txt --- a/test-data/out4.imzml.txt Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out4.imzml.txt Sun Sep 27 11:10:30 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 44 --rw-rw-r-- 1 meli meli 28792 Aug 23 17:39 ibd --rw-rw-r-- 1 meli meli 12046 Aug 23 17:39 imzml +-rw-rw-r-- 1 meli meli 28792 Sep 27 10:52 ibd +-rw-rw-r-- 1 meli meli 12046 Sep 27 10:52 imzml |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out5.imzml --- a/test-data/out5.imzml Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out5.imzml Sun Sep 27 11:10:30 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="30751422-deca-429e-9f8e-24639c108d6d" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2c7f19c6447844039a112152c19f7cfd50dbf12e" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="37236c7e-6e93-4ccc-9111-1b1153aac713" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ccb886aaf3cb7564f518884413ea988c59a1de57" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out5.imzml.txt --- a/test-data/out5.imzml.txt Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out5.imzml.txt Sun Sep 27 11:10:30 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 20 --rw-rw-r-- 1 meli meli 380 Aug 23 17:40 ibd --rw-rw-r-- 1 meli meli 13525 Aug 23 17:40 imzml +-rw-rw-r-- 1 meli meli 380 Sep 27 10:53 ibd +-rw-rw-r-- 1 meli meli 13525 Sep 27 10:53 imzml |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out6.imzml --- a/test-data/out6.imzml Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out6.imzml Sun Sep 27 11:10:30 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="254b991f-92f5-46d5-8069-6f9ecd53b05a" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0aaa784dc2a335da176a4bc2d12a43f2d18bdbf1" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="734d4b50-4440-4747-a0e9-de78974d1487" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="b1636b28fd4e0ab9caf5aaa4c1a40760030a4e73" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out6.imzml.txt --- a/test-data/out6.imzml.txt Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out6.imzml.txt Sun Sep 27 11:10:30 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 164 --rw-rw-r-- 1 meli meli 146896 Aug 23 17:41 ibd --rw-rw-r-- 1 meli meli 18221 Aug 23 17:41 imzml +-rw-rw-r-- 1 meli meli 146896 Sep 27 10:53 ibd +-rw-rw-r-- 1 meli meli 18221 Sep 27 10:53 imzml |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out7.imzml --- a/test-data/out7.imzml Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out7.imzml Sun Sep 27 11:10:30 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="227ecc2e-a494-4018-afc5-45eaa790e812" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="e22162d1dd762607ca6d31c0b8892e0ae5a3a772" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="f81632b3-50b0-4a57-88a2-5f7cf97f9bae" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9f88294c3cff3e8c30e80632d6ad616b7db18089" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out7.imzml.txt --- a/test-data/out7.imzml.txt Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out7.imzml.txt Sun Sep 27 11:10:30 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 116 --rw-rw-r-- 1 meli meli 95976 Aug 23 17:41 ibd --rw-rw-r-- 1 meli meli 18199 Aug 23 17:41 imzml +-rw-rw-r-- 1 meli meli 95976 Sep 27 10:54 ibd +-rw-rw-r-- 1 meli meli 18199 Sep 27 10:54 imzml |
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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out8.imzml --- a/test-data/out8.imzml Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out8.imzml Sun Sep 27 11:10:30 2020 +0000 |
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| b'@@ -9,9 +9,9 @@\n \t\t<fileContent>\n \t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="91ed729b-0b8d-49f6-b832-e4d3834fe733" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="efd09bddeebeb334efe9dffad3a4f3bed35442d1" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="02059ae7-7beb-4ecf-92ae-7a767e04bf43" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="dc3960918fa3008824889b4ac142be1d0534ded8" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n \t<referenceableParamGroupList count="4">\n@@ -90,15 +90,15 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| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/out8.imzml.txt --- a/test-data/out8.imzml.txt Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out8.imzml.txt Sun Sep 27 11:10:30 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ imzML file: -total 348 --rw-rw-r-- 1 meli meli 335976 Aug 23 17:42 ibd --rw-rw-r-- 1 meli meli 12402 Aug 23 17:42 imzml +total 260 +-rw-rw-r-- 1 meli meli 248824 Sep 27 11:44 ibd +-rw-rw-r-- 1 meli meli 12397 Sep 27 11:44 imzml |
| b |
| diff -r ca727a6dede6 -r 5abc3ab4792c test-data/rdata_notfiltered.pdf |
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| Binary file test-data/rdata_notfiltered.pdf has changed |