| Next changeset 1:98c101b19f3c (2018-04-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f |
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added:
msi_filtering.xml test-data/Analyze75.hdr test-data/Analyze75.img test-data/Analyze75.t2m test-data/Example_Continuous.ibd test-data/Example_Continuous.imzML test-data/analyze_filtered.RData test-data/analyze_filtered.pdf test-data/analyze_matrix.tabular test-data/analyze_originaloutput.RData test-data/featuresofinterest2.tabular test-data/imzml_filtered.RData test-data/imzml_filtered.pdf test-data/inputfeatures.tabular test-data/inputpixels.tabular test-data/inputpixels2.tabular test-data/preprocessing_results1.RData test-data/rdata_matrix.tabular |
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| diff -r 000000000000 -r f17d3f1a065f msi_filtering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msi_filtering.xml Wed Feb 28 14:02:21 2018 -0500 |
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| b'@@ -0,0 +1,361 @@\n+<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.7.0">\n+ <description>tool for filtering mass spectrometry imaging data</description>\n+ <requirements>\n+ <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>\n+ <requirement type="package" version="2.2.1">r-gridextra</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+\n+ #if $infile.ext == \'imzml\'\n+ cp \'${infile.extra_files_path}/imzml\' infile.imzML &&\n+ cp \'${infile.extra_files_path}/ibd\' infile.ibd &&\n+ #elif $infile.ext == \'analyze75\'\n+ cp \'${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 $infile infile.RData &&\n+ #end if\n+ cat \'${MSI_subsetting}\' &&\n+ echo ${MSI_subsetting} &&\n+ Rscript \'${MSI_subsetting}\'\n+\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="MSI_subsetting"><![CDATA[\n+\n+\n+################################# load libraries and read file #########################\n+\n+\n+library(Cardinal)\n+library(gridExtra)\n+\n+## Read MALDI Imaging dataset\n+\n+#if $infile.ext == \'imzml\'\n+ msidata = readMSIData(\'infile.imzML\')\n+#elif $infile.ext == \'analyze75\'\n+ msidata = readMSIData(\'infile.hdr\')\n+#else\n+ load(\'infile.RData\')\n+#end if\n+\n+###################################### inputfile properties in numbers ######################\n+\n+#if $outputs.outputs_select == "quality_control"\n+ ## Number of features (mz)\n+ maxfeatures = length(features(msidata))\n+ ## Range mz\n+ minmz = round(min(mz(msidata)), digits=2)\n+ maxmz = round(max(mz(msidata)), digits=2)\n+ ## Number of spectra (pixels)\n+ pixelcount = length(pixels(msidata))\n+ ## Range x coordinates\n+ minimumx = min(coord(msidata)[,1])\n+ maximumx = max(coord(msidata)[,1])\n+ ## Range y coordinates\n+ minimumy = min(coord(msidata)[,2])\n+ maximumy = max(coord(msidata)[,2])\n+ ## Number of intensities > 0\n+ npeaks= sum(spectra(msidata)[]>0)\n+ ## Spectra multiplied with mz (potential number of peaks)\n+ numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])\n+ ## Percentage of intensities > 0\n+ percpeaks = round(npeaks/numpeaks*100, digits=2)\n+ ## Number of empty TICs\n+ TICs = colSums(spectra(msidata)[])\n+ NumemptyTIC = sum(TICs == 0)\n+ ## median TIC\n+ medint = round(median(TICs), digits=2)\n+ ## Store features for QC plot\n+ featuresinfile = mz(msidata)\n+#end if\n+\n+\n+###################################### filtering of pixels ######################\n+#if $inputpixels:\n+ input_list = read.delim("$inputpixels", header = FALSE, \n+ na.strings=c("","NA", "#NUM!", "#ZAHL!"), stringsAsFactors = FALSE)\n+ validpixels = input_list[,$pixel_column] %in% names(pixels(msidata))\n+\n+ if (validpixels != 0)\n+ {\n+ pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[validpixels,$pixel_column]]\n+ msidata = msidata[,pixelsofinterest]\n+ numberpixels = length(input_list[,$pixel_column])\n+ }else {\n+ numberpixels = 0\n+ }\n+\n+\n+#else\n+ input_list = data.frame(0, 0)\n+ validpixels=0\n+ numberpixels = 0\n+#end if\n+\n+\n+\n+###################################### filtering of features ######################\n+\n+#if $inputfeatures:\n+ input_features = read.delim("$inputfeatures", header = FALSE,\n+ na.strings=c("","NA", "#NUM!", "#ZAHL!"), stringsAsFactors = FALSE)\n+ validfeatures = input_features[,$feature_column] %in% names(features(msidata)) \n+\n+ if (validfeatures != 0)\n+ {\n+ featuresofinterest = features(msidata)[names(features(msidata)) %in% input_features[validfeatures,$feature_column]]\n+ msidata = msidata[featuresofinterest,]\n+ '..b'lue="Example_Continuous.imzML"/>\n+ <composite_data value="Example_Continuous.ibd"/>\n+ </param>\n+ <param name="inputpixels" ftype="tabular" value = "inputpixels.tabular"/>\n+ <param name="pixel_column" value="1"/>\n+ <param name="inputfeatures" ftype="tabular" value = "inputfeatures.tabular"/>\n+ <param name="feature_column" value="2"/>\n+\n+ <conditional name="outputs">\n+ <param name="outputs_select" value="quality_control"/>\n+ <param name="inputmz" value="328.9"/>\n+ <param name="plusminus_dalton" value="0.25"/>\n+ </conditional>\n+ <output name="filtering_qc" file="imzml_filtered.pdf" compare="sim_size" delta="20000"/>\n+ <output name="msidata_filtered" file="imzml_filtered.RData" compare="sim_size" />\n+ </test>\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+ <composite_data value="Analyze75.t2m"/>\n+ </param>\n+ <param name="inputpixels" ftype="tabular" value = "inputpixels2.tabular"/>\n+ <param name="pixel_column" value="1"/>\n+ <param name="inputfeatures" ftype="tabular" value = "featuresofinterest2.tabular"/>\n+ <param name="feature_column" value="1"/>\n+ <conditional name="outputs">\n+ <param name="outputs_select" value="quality_control"/>\n+ <param name="inputmz" value="702"/>\n+ <param name="plusminus_dalton" value="0.25"/>\n+ </conditional>\n+ <param name="output_matrix" value="True"/>\n+ <output name="filtering_qc" file="analyze_filtered.pdf" compare="sim_size" delta="20000"/>\n+ <output name="msidata_filtered" file="analyze_filtered.RData" compare="sim_size" />\n+ <output name="matrixasoutput" file="analyze_matrix.tabular"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="infile" value="" ftype="analyze75">\n+ <composite_data value="Analyze75.hdr"/>\n+ <composite_data value="Analyze75.img"/>\n+ <composite_data value="Analyze75.t2m"/>\n+ </param>\n+ <conditional name="outputs">\n+ <param name="outputs_select" value="no_quality_control"/>\n+ </conditional>\n+ <output name="msidata_filtered" file="analyze_originaloutput.RData" compare="sim_size" />\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>\n+ <conditional name="outputs">\n+ <param name="outputs_select" value="no_quality_control"/>\n+ </conditional>\n+ <param name="output_matrix" value="True"/>\n+ <output name="matrixasoutput" file="rdata_matrix.tabular"/>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+\n+This tool can filter three types of mass-spectrometry imaging files (see below) for pixels and features of interest. This can be used to keep only pixels in a regions of interest.\n+For filtering at least one valid pixel/feature is needed otherwise no filtering will be performed.\n+\n+Input 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 <http://ms-imaging.org/wp/introduction/>`_\n+- Analyze7.5 (upload hdr, img and t2m file via the "composite" function)\n+- Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)\n+\n+The output of this tool is a subsetted Cardinal "MSImageSet" with the variable name "msidata" saved as .RData. \n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btv146</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r f17d3f1a065f test-data/Example_Continuous.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Example_Continuous.imzML Wed Feb 28 14:02:21 2018 -0500 |
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| b'@@ -0,0 +1,373 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\r\n+<mzML xmlns="http://psi.hupo.org/ms/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_idx.xsd" version="1.1">\r\n+ <cvList count="3">\r\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo"/>\r\n+ <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\r\n+ <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>\r\n+ </cvList>\r\n+ <fileDescription>\r\n+ <fileContent>\r\n+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{554A27FA-79D2-4766-9A2C-862E6D78B1F3}"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="A5BE532D25997B71BE6D20C76561DDC4D5307DDD"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value=""/>\r\n+ </fileContent>\r\n+ <sourceFileList count="1">\r\n+ <sourceFile id="sf1" name="Example.raw" location="C:\\Users\\Thorsten Schramm\\Documents\\Promotion\\imzML\\Website\\files\\Beispiel-Dateien\\Example images\\">\r\n+ <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW file" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>\r\n+ </sourceFile>\r\n+ </sourceFileList>\r\n+ <contact>\r\n+ <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>\r\n+ <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institut f\xfcr Anorganische und Analytische Chemie"/>\r\n+ <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstra\xdfe 60, Haus 16, Gie\xdfen, Germany"/>\r\n+ <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>\r\n+ </contact>\r\n+ </fileDescription>\r\n+ <referenceableParamGroupList count="4">\r\n+ <referenceableParamGroup id="mzArray">\r\n+ <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\r\n+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>\r\n+ </referenceableParamGroup>\r\n+ <referenceableParamGroup id="intensityArray">\r\n+ <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\r\n+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>\r\n+ </referenceableParamGroup>\r\n+ <referenceableParamGroup id="scan1">\r\n+ <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000095" name="linear" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - 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| @@ -0,0 +1,102 @@ + x = 1, y = 1 x = 3, y = 1 x = 1, y = 2 x = 3, y = 2 x = 1, y = 3 +701.317626953125 1 0 0 0 0 +701.333435058594 2 0 0 0 0 +701.349243164062 2 0 0 0 0 +701.365051269531 3 0 0 0 0 +701.380859375 1 1 0 0 0 +701.396667480469 1 0 1 0 0 +701.412475585938 2 0 0 0 0 +701.428283691406 5 0 0 0 0 +701.444091796875 6 0 0 0 0 +701.459899902344 2 0 0 0 0 +701.475708007812 1 1 0 0 0 +701.491516113281 1 0 0 0 0 +701.50732421875 1 1 0 0 0 +701.523132324219 0 0 0 0 0 +701.538940429688 1 1 0 0 0 +701.554748535156 1 0 0 0 1 +701.570617675781 1 0 0 0 0 +701.58642578125 1 0 0 0 0 +701.602233886719 1 0 0 0 0 +701.618041992188 0 1 0 0 0 +701.633850097656 1 1 0 0 1 +701.649658203125 0 1 0 0 0 +701.665466308594 1 1 0 1 1 +701.681274414062 1 2 0 0 0 +701.697082519531 0 0 0 0 1 +701.712890625 2 0 0 0 1 +701.728759765625 3 0 0 0 0 +701.744567871094 1 1 0 1 0 +701.760375976562 1 2 0 0 0 +701.776184082031 0 1 0 1 0 +701.7919921875 0 0 0 0 1 +701.807800292969 0 0 0 0 0 +701.823608398438 2 0 1 0 0 +701.839416503906 3 1 0 1 0 +701.855224609375 4 1 0 0 1 +701.87109375 3 0 0 1 0 +701.886901855469 1 0 0 0 0 +701.902709960938 1 1 0 1 0 +701.918518066406 3 0 0 0 0 +701.934326171875 3 0 0 1 0 +701.950134277344 4 1 0 1 0 +701.965942382812 6 1 0 2 1 +701.981811523438 5 0 0 1 0 +701.997619628906 1 0 0 0 0 +702.013427734375 1 0 0 0 0 +702.029235839844 0 0 0 0 1 +702.045043945312 0 1 0 0 0 +702.060852050781 1 0 0 0 0 +702.076721191406 0 0 0 0 0 +702.092529296875 0 0 0 1 1 +702.108337402344 1 0 1 0 0 +702.124145507812 1 0 2 0 0 +702.139953613281 1 0 0 0 1 +702.15576171875 2 0 0 0 1 +702.171630859375 0 0 0 1 1 +702.187438964844 0 0 0 0 0 +702.203247070312 0 0 0 0 0 +702.219055175781 1 1 0 1 0 +702.23486328125 1 0 1 0 0 +702.250732421875 0 1 0 0 0 +702.266540527344 0 0 0 0 0 +702.282348632812 2 0 0 1 0 +702.298156738281 4 1 0 1 0 +702.31396484375 7 1 0 0 0 +702.329833984375 5 0 0 0 0 +702.345642089844 3 0 0 0 0 +702.361450195312 2 0 0 0 0 +702.377258300781 2 1 0 0 0 +702.393127441406 2 1 0 0 1 +702.408935546875 1 0 0 1 0 +702.424743652344 1 0 0 0 0 +702.440551757812 1 0 0 0 0 +702.456420898438 0 0 0 0 0 +702.472229003906 0 1 0 0 0 +702.488037109375 0 2 0 0 1 +702.503845214844 1 2 1 1 0 +702.519714355469 1 1 1 0 0 +702.535522460938 0 0 0 0 0 +702.551330566406 2 0 0 0 0 +702.567138671875 3 0 0 1 0 +702.5830078125 4 0 0 1 0 +702.598815917969 1 1 0 1 0 +702.614624023438 2 1 0 0 0 +702.630432128906 2 1 0 0 0 +702.646301269531 2 0 1 1 1 +702.662109375 1 0 1 0 1 +702.677917480469 0 0 1 2 0 +702.693725585938 0 0 0 3 1 +702.709594726562 1 0 1 2 0 +702.725402832031 2 0 0 1 0 +702.7412109375 3 0 0 0 0 +702.757080078125 2 1 0 0 1 +702.772888183594 2 1 0 1 0 +702.788696289062 5 0 0 0 0 +702.804565429688 7 0 0 0 0 +702.820373535156 5 1 0 0 0 +702.836181640625 3 0 0 0 0 +702.851989746094 2 0 0 0 1 +702.867858886719 1 0 0 0 0 +702.883666992188 2 0 0 0 0 +702.899475097656 5 1 0 0 1 |
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| diff -r 000000000000 -r f17d3f1a065f test-data/featuresofinterest2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/featuresofinterest2.tabular Wed Feb 28 14:02:21 2018 -0500 |
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| @@ -0,0 +1,101 @@ +"m/z = 701.32" +"m/z = 701.33" +"m/z = 701.35" +"m/z = 701.37" +"m/z = 701.38" +"m/z = 701.4" +"m/z = 701.41" +"m/z = 701.43" +"m/z = 701.44" +"m/z = 701.46" +"m/z = 701.48" +"m/z = 701.49" +"m/z = 701.51" +"m/z = 701.52" +"m/z = 701.54" +"m/z = 701.55" +"m/z = 701.57" +"m/z = 701.59" +"m/z = 701.6" +"m/z = 701.62" +"m/z = 701.63" +"m/z = 701.65" +"m/z = 701.67" +"m/z = 701.68" +"m/z = 701.7" +"m/z = 701.71" +"m/z = 701.73" +"m/z = 701.74" +"m/z = 701.76" +"m/z = 701.78" +"m/z = 701.79" +"m/z = 701.81" +"m/z = 701.82" +"m/z = 701.84" +"m/z = 701.86" +"m/z = 701.87" +"m/z = 701.89" +"m/z = 701.9" +"m/z = 701.92" +"m/z = 701.93" +"m/z = 701.95" +"m/z = 701.97" +"m/z = 701.98" +"m/z = 702" +"m/z = 702.01" +"m/z = 702.03" +"m/z = 702.05" +"m/z = 702.06" +"m/z = 702.08" +"m/z = 702.09" +"m/z = 702.11" +"m/z = 702.12" +"m/z = 702.14" +"m/z = 702.16" +"m/z = 702.17" +"m/z = 702.19" +"m/z = 702.2" +"m/z = 702.22" +"m/z = 702.23" +"m/z = 702.25" +"m/z = 702.27" +"m/z = 702.28" +"m/z = 702.3" +"m/z = 702.31" +"m/z = 702.33" +"m/z = 702.35" +"m/z = 702.36" +"m/z = 702.38" +"m/z = 702.39" +"m/z = 702.41" +"m/z = 702.42" +"m/z = 702.44" +"m/z = 702.46" +"m/z = 702.47" +"m/z = 702.49" +"m/z = 702.5" +"m/z = 702.52" +"m/z = 702.54" +"m/z = 702.55" +"m/z = 702.57" +"m/z = 702.58" +"m/z = 702.6" +"m/z = 702.61" +"m/z = 702.63" +"m/z = 702.65" +"m/z = 702.66" +"m/z = 702.68" +"m/z = 702.69" +"m/z = 702.71" +"m/z = 702.73" +"m/z = 702.74" +"m/z = 702.76" +"m/z = 702.77" +"m/z = 702.79" +"m/z = 702.8" +"m/z = 702.82" +"m/z = 702.84" +"m/z = 702.85" +"m/z = 702.87" +"m/z = 702.88" +"m/z = 702.9" |
| b |
| diff -r 000000000000 -r f17d3f1a065f test-data/imzml_filtered.RData |
| b |
| Binary file test-data/imzml_filtered.RData has changed |
| b |
| diff -r 000000000000 -r f17d3f1a065f test-data/imzml_filtered.pdf |
| b |
| Binary file test-data/imzml_filtered.pdf has changed |
| b |
| diff -r 000000000000 -r f17d3f1a065f test-data/inputfeatures.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputfeatures.tabular Wed Feb 28 14:02:21 2018 -0500 |
| b |
| @@ -0,0 +1,17 @@ + m/z = 100.08 + m/z = 100.17 + m/z = 100.25 + m/z = 100.33 + m/z = 100.42 + m/z = 100.5 + m/z = 799.5 + m/z = 799.58 + m/z = 799.67 + m/z = 799.75 + m/z = 799.8 + m/z = 799.83 + m/z = 799.92 + m/z = 328.92 + m/z = 329 + m/z = 329.08 + m/z = 328.83 |
| b |
| diff -r 000000000000 -r f17d3f1a065f test-data/inputpixels.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpixels.tabular Wed Feb 28 14:02:21 2018 -0500 |
| b |
| @@ -0,0 +1,6 @@ +x = 1, y = 1 +x = 1, y = 2 +x = 1, y = 3 +x = 3, y = 1 +x = 3, y = 2 +x = 3, y = 3 |
| b |
| diff -r 000000000000 -r f17d3f1a065f test-data/inputpixels2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpixels2.tabular Wed Feb 28 14:02:21 2018 -0500 |
| b |
| @@ -0,0 +1,5 @@ +x = 1, y = 1 +x = 1, y = 2 +x = 1, y = 3 +x = 3, y = 2 +x = 3, y = 1 |
| b |
| diff -r 000000000000 -r f17d3f1a065f test-data/preprocessing_results1.RData |
| b |
| Binary file test-data/preprocessing_results1.RData has changed |
| b |
| diff -r 000000000000 -r f17d3f1a065f test-data/rdata_matrix.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdata_matrix.tabular Wed Feb 28 14:02:21 2018 -0500 |
| b |
| b'@@ -0,0 +1,8400 @@\n+\tx = 1, y = 1\tx = 2, y = 1\tx = 3, y = 1\tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 2\tx = 1, y = 3\tx = 2, y = 3\tx = 3, y = 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|