| Previous changeset 4:42580292d381 (2018-06-11) Next changeset 6:d3fd539f477e (2018-06-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 |
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modified:
msi_preprocessing.xml test-data/preprocessing_results1.RData test-data/preprocessing_results1.txt test-data/preprocessing_results2.RData test-data/preprocessing_results2.pdf test-data/preprocessing_results3.RData test-data/preprocessing_results3.pdf test-data/preprocessing_results4.RData test-data/preprocessing_results5.RData test-data/preprocessing_results5.pdf |
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added:
test-data/123_combined.RData test-data/preprocessing_mean3.txt test-data/preprocessing_median2.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results4.pdf test-data/preprocessing_sd2.txt |
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removed:
test-data/preprocessed.RData |
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| diff -r 42580292d381 -r 2fccfd11360d msi_preprocessing.xml --- a/msi_preprocessing.xml Mon Jun 11 17:34:07 2018 -0400 +++ b/msi_preprocessing.xml Tue Jun 19 18:08:01 2018 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.1">\n+<tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.2">\n <description>\n mass spectrometry imaging preprocessing\n </description>\n@@ -6,7 +6,7 @@\n <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>\n <requirement type="package" version="2.2.1">r-gridextra</requirement>\n <requirement type="package" version="0.20-35">r-lattice</requirement>\n- <requirement type="package" version="3.34.9">bioconductor-limma</requirement>\n+ <!--requirement type="package" version="3.34.9">bioconductor-limma</requirement-->\n </requirements>\n <command detect_errors="exit_code">\n <![CDATA[\n@@ -34,10 +34,10 @@\n library(Cardinal)\n library(gridExtra)\n library(lattice)\n-library(limma)\n+###library(limma)\n \n #if $infile.ext == \'imzml\'\n- msidata = readImzML(\'infile\')\n+ msidata <- readImzML(\'infile\', mass.accuracy=$accuracy, units.accuracy = "$units")\n #elif $infile.ext == \'analyze75\'\n msidata = readAnalyze(\'infile\')\n #else\n@@ -52,45 +52,14 @@\n get(ls()[ls() != "fileName"])\n }\n \n-######################### preparations for optional QC report #################\n-\n-#if $outputs.outputs_select == "quality_control":\n-\n- ### values for QC table:\n+######################### preparations for QC report #################\n \n maxfeatures = length(features(msidata))\n medianpeaks = median(colSums(spectra(msidata)[]>0))\n medint = round(median(spectra(msidata)[]), digits=2)\n TICs = round(mean(colSums(spectra(msidata)[])), digits=1)\n- QC_numbers= data.frame(rawdata = c(maxfeatures, medianpeaks, medint, TICs))\n- vectorofactions = "rawdata"\n-\n- ### Read tabular file with calibrant m/z: \n-\n- calibrant_list = read.delim("$outputs.calibrant_file", header = FALSE, stringsAsFactors = FALSE)\n-\n- ### calculate how many input calibrant m/z are valid: \n-\n- inputcalibrants = calibrant_list[calibrant_list[,$outputs.calibrants_column]>min(mz(msidata)) & calibrant_list[,$outputs.calibrants_column]<max(mz(msidata)),$outputs.calibrants_column]\n- number_calibrants_in = length(calibrant_list[,$outputs.calibrants_column])\n- number_calibrants_valid = length(inputcalibrants)\n-\n- ### Quality control report\n-\n- pdf("Preprocessing.pdf", fonts = "Times", pointsize = 12)\n- plot(0,type=\'n\',axes=FALSE,ann=FALSE)\n- title(main=paste("Quality control during preprocessing \\n", "Filename:", "$infile.display_name"))\n- title(main=paste0("\\n\\n\\n\\n Number valid m/z in ", "$outputs.calibrant_file.display_name",": ", number_calibrants_valid, "/", number_calibrants_in))\n-\n- for (calibrant in inputcalibrants)\n- {currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",\n- par.strip.text=list(col="black", cex=.9)),lattice=TRUE, \n- scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="raw")\n- assign(paste("rawdata",calibrant, sep="_"), currentimage)}\n-\n- current_plot_raw = vector(length(inputcalibrants), mode=\'list\')\n-\n-#end if\n+ QC_numbers= data.frame(inputdata = c(maxfeatures, medianpeaks, medint, TICs))\n+ vectorofactions = "inputdata"\n \n ############################### Preprocessing steps ###########################\n ###############################################################################\n@@ -105,27 +74,15 @@\n \n msidata = normalize(msidata, method="tic")\n \n- ############################### optional QC ###########################\n+ ############################### QC ###########################\n \n- #if $outputs.outputs_select == "quality_control":\n-\n- ### values for QC table:\n maxfeatures = length(features(msidata))\n medianpeaks = median(colSums(spectra(msidata)[]>0))\n medint = round(median(spectra(msidata)[]), dig'..b'\n- <param name="calibrants_column" value="1"/>\n- <param name="plusminus_dalton" value="0.25"/>\n- <param name="output_matrix" value="True"/>\n+ <param name="summary_type" value="median,sd"/>\n <output name="msidata_preprocessed" file="preprocessing_results2.RData" compare="sim_size"/>\n- <output name="matrixasoutput" file="preprocessing_results2.txt" lines_diff="2"/>\n+ <output name="summarized_output_median" file="preprocessing_median2.txt" lines_diff="2"/>\n+ <output name="summarized_output_sd" file="preprocessing_sd2.txt" lines_diff="2"/>\n <output name="QC_plots" file="preprocessing_results2.pdf" compare="sim_size"/>\n </test>\n- <test expect_num_outputs="2">\n+ <test expect_num_outputs="3">\n <param name="infile" value="" ftype="analyze75">\n <composite_data value="Analyze75.hdr"/>\n <composite_data value="Analyze75.img"/>\n@@ -819,14 +723,12 @@\n </conditional>\n </conditional>\n </repeat>\n- <param name="outputs_select" value="quality_control"/>\n- <param name="calibrant_file" ftype="tabular" value="inputcalibrantfile2.tabular"/>\n- <param name="calibrants_column" value="1"/>\n- <param name="plusminus_dalton" value="0.25"/>\n+ <param name="summary_type" value="mean"/>\n <output name="msidata_preprocessed" file="preprocessing_results3.RData" compare="sim_size"/>\n <output name="QC_plots" file="preprocessing_results3.pdf" compare="sim_size"/>\n+ <output name="summarized_output_mean" file="preprocessing_mean3.txt" lines_diff="2"/>\n </test>\n- <test expect_num_outputs="2">\n+ <test expect_num_outputs="3">\n <param name="infile" value="" ftype="analyze75">\n <composite_data value="Analyze75.hdr"/>\n <composite_data value="Analyze75.img"/>\n@@ -843,12 +745,12 @@\n <param name="bin_width" value="0.1"/>\n </conditional>\n </repeat>\n- <param name="outputs_select" value="no_quality_control"/>\n <param name="output_matrix" value="True"/>\n <output name="msidata_preprocessed" file="preprocessing_results4.RData" compare="sim_size"/>\n <output name="matrixasoutput" file="preprocessing_results4.txt"/>\n+ <output name="QC_plots" file="preprocessing_results4.pdf" compare="sim_size"/>\n </test>\n- <test expect_num_outputs="3">\n+ <test expect_num_outputs="2">\n <param name="infile" value="" ftype="imzml">\n <composite_data value="Example_Continuous.imzML"/>\n <composite_data value="Example_Continuous.ibd"/>\n@@ -862,13 +764,7 @@\n </conditional>\n </conditional>\n </repeat>\n- <param name="outputs_select" value="quality_control"/>\n- <param name="calibrant_file" ftype="tabular" value="inputcalibrantfile1.tabular"/>\n- <param name="calibrants_column" value="1"/>\n- <param name="plusminus_dalton" value="0.25"/>\n- <param name="output_matrix" value="True"/>\n- <output name="msidata_preprocessed" file="preprocessing_results5.RData" compare="sim_size"/>\n- <output name="matrixasoutput" file="preprocessing_results5.txt"/>\n+ <output name="msidata_preprocessed" file="preprocessing_results5.RData" compare="sim_size"/>\n <output name="QC_plots" file="preprocessing_results5.pdf" compare="sim_size"/>\n </test>\n </tests>\n@@ -899,7 +795,7 @@\n Output: \n \n - imzML file, preprocessed\n-- optional: pdf with heatmap of m/z of interest after each preprocessing step\n+- pdf with key values after each processing step\n - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)\n \n Tip: \n' |
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| diff -r 42580292d381 -r 2fccfd11360d test-data/123_combined.RData |
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| Binary file test-data/123_combined.RData has changed |
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| diff -r 42580292d381 -r 2fccfd11360d test-data/preprocessed.RData |
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| Binary file test-data/preprocessed.RData has changed |
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| diff -r 42580292d381 -r 2fccfd11360d test-data/preprocessing_mean3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/preprocessing_mean3.txt Tue Jun 19 18:08:01 2018 -0400 |
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| b'@@ -0,0 +1,356 @@\n+\tUploaded Composite Dataset 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| diff -r 42580292d381 -r 2fccfd11360d test-data/preprocessing_median2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/preprocessing_median2.txt Tue Jun 19 18:08:01 2018 -0400 |
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| @@ -1,3 +1,3 @@ x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3 -329 71.9222398089711 36.0331719015123 0 0 52.1631651555205 44.6843848381426 0 0 0 -345 0 0 22.145861000629 0 0 0 27.3529366713824 17.4681423285726 25.8629113644351 +329 8.48069807321137 6.00276368862812 0 0 7.22240715797167 6.68463797360356 0 0 0 +345 0 0 4.70593890744759 0 0 0 5.23000350586712 4.17949067812964 5.08555910047608 |
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