| Next changeset 1:c4abf42419c2 (2017-11-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 |
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msi_preprocessing.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/LM5_first68pixel.RData test-data/preprocessing_results1.RData test-data/preprocessing_results1.csv test-data/preprocessing_results2.RData test-data/preprocessing_results2.csv test-data/preprocessing_results3.RData test-data/preprocessing_results3.csv |
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| diff -r 000000000000 -r 74fcb3c95a53 msi_preprocessing.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msi_preprocessing.xml Tue Oct 31 15:05:05 2017 -0400 |
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| b'@@ -0,0 +1,340 @@\n+<tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.7.0">\n+ <description>\n+ mass spectrometry imaging preprocessing\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="1.7.0">bioconductor-cardinal</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 \'$infile\' infile.RData &&\n+ #end if\n+ cat \'${cardinal_preprocessing}\' &&\n+ Rscript \'${cardinal_preprocessing}\'\n+\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="cardinal_preprocessing"><![CDATA[\n+library(Cardinal)\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+maxpixel = length(pixels(msidata)) \n+pixelnumber = c(1:maxpixel)\n+\n+#for $method in $methods:\n+ #if str( $method.methods_conditional.preprocessing_method ) == \'Normalization\':\n+ print(\'Normalization\')\n+ ##normalization\n+ msidata <- normalize(msidata, pixel=pixelnumber, method="tic")\n+\n+ #elif str( $method.methods_conditional.preprocessing_method ) == \'Baseline_reduction\':\n+ print(\'Baseline_reduction\')\n+ ##baseline reduction\n+ msidata = reduceBaseline(msidata, pixel=pixelnumber, method="median", blocks=$method.methods_conditional.blocks_baseline)\n+\n+ #elif str( $method.methods_conditional.preprocessing_method ) == \'Smoothing\':\n+ print(\'Smoothing\')\n+ ## Smoothing\n+\n+ #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == \'gaussian\':\n+ print(\'gaussian smoothing\')\n+ msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian)\n+ #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == \'sgolay\':\n+ print(\'sgolay smoothing\')\n+ msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters)\n+ #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == \'ma\':\n+ print(\'sgolay smoothing\')\n+ msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter)\n+ #end if\n+\n+ #elif str( $method.methods_conditional.preprocessing_method) == \'Peak_picking\':\n+ print(\'Peak_picking\')\n+ ## Peakpicking\n+\n+ #if str( $method.methods_conditional.methods_for_picking.picking_method) == \'adaptive\':\n+ print(\'adaptive peakpicking\')\n+ msidata = peakPick(msidata, pixel=pixelnumber, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method=\'$method.methods_conditional.methods_for_picking.picking_method\', SNR=$method.methods_conditional.SNR_picking_method, spar=$method.methods_conditional.methods_for_picking.spar_picking)\n+\n+ #elif str( $method.methods_conditional.methods_for_picking.picking_method) == \'limpic\':\n+ print(\'limpic peakpicking\')\n+ msidata '..b'ethods_conditional">\n+ <param name="preprocessing_method" value="Baseline_reduction" />\n+ <param name="blocks_baseline" value="50" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="methods">\n+ <conditional name="methods_conditional">\n+ <param name="preprocessing_method" value="Peak_picking" />\n+ <param name="blocks_picking" value="3" />\n+ <param name="window_picking" value="5" />\n+ <param name="methods_for_picking" value="simple" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="methods">\n+ <conditional name="methods_conditional">\n+ <param name="preprocessing_method" value="Peak_alignment" />\n+ <param name="methods_for_alignment" value="DP" />\n+ </conditional>\n+ </repeat>\n+ <output name="msidata_preprocessed" file="preprocessing_results2.RData" compare="sim_size" />\n+ <output name="preprocessed_intensity_matrix" file="preprocessing_results2.csv" lines_diff="2"/>\n+ </test>\n+ <test>\n+ <param name="infile" value="" ftype="analyze75">\n+ <composite_data value="Analyze75.hdr" ftype="hdr"/>\n+ <composite_data value="Analyze75.img" ftype="img"/>\n+ <composite_data value="Analyze75.t2m" ftype="t2m"/>\n+ </param>\n+ <repeat name="methods">\n+ <conditional name="methods_conditional">\n+ <param name="preprocessing_method" value="Normalization" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="methods">\n+ <conditional name="methods_conditional">\n+ <param name="preprocessing_method" value="Smoothing" />\n+ <conditional name="methods_for_smoothing">\n+ <param name="smoothing_method" value="gaussian" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <repeat name="methods">\n+ <conditional name="methods_conditional">\n+ <param name="preprocessing_method" value="Peak_picking" />\n+ <param name="blocks_picking" value="3" />\n+ <param name="window_picking" value="5" />\n+ <param name="methods_for_picking" value="limpic" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="methods">\n+ <conditional name="methods_conditional">\n+ <param name="preprocessing_method" value="Peak_alignment" />\n+ <param name="methods_for_alignment" value="diff" />\n+ </conditional>\n+ </repeat>\n+ <output name="msidata_preprocessed" file="preprocessing_results3.RData" compare="sim_size" />\n+ <output name="preprocessed_intensity_matrix" file="preprocessing_results3.csv" />\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets.\n+\n+**Preprocessing steps:**\n+\n+- Smoothening: Smoothing of the mass peaks reduces noise and improves peak detection\n+- Normalization: Normalization of intensities to total ion current (TIC)\n+- Baseline reduction: Baseline reduction removes backgroundintensity generated by chemical noise (common in MALDI datasets)\n+- Peak picking: relevant peaks are picked while noise-peaks are removed\n+- Peak alignment: mz inaccuracies are removed by alignment of same peaks to a common mz value\n+- Peak filtering: removes peaks that occur infrequently, such as those which only occur in a small proportion of pixels\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 74fcb3c95a53 test-data/Example_Continuous.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Example_Continuous.imzML Tue Oct 31 15:05:05 2017 -0400 |
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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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|
| b |
| diff -r 000000000000 -r 74fcb3c95a53 test-data/preprocessing_results2.RData |
| b |
| Binary file test-data/preprocessing_results2.RData has changed |
| b |
| diff -r 000000000000 -r 74fcb3c95a53 test-data/preprocessing_results2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/preprocessing_results2.csv Tue Oct 31 15:05:05 2017 -0400 |
| b |
| b'@@ -0,0 +1,4245 @@\n+"","x = 1, y = 1","x = 2, y = 1","x = 3, y = 1","x = 4, y = 1","x = 5, y = 1","x = 6, y = 1","x = 7, y = 1","x = 8, y = 1","x = 9, y = 1","x = 10, y = 1","x = 11, y = 1","x = 12, y = 1","x = 13, y = 1","x = 14, y = 1","x = 15, y = 1","x = 16, y = 1","x = 17, y = 1","x = 1, y = 2","x = 2, y = 2","x = 3, y = 2","x = 4, y = 2","x = 5, y = 2","x = 6, y = 2","x = 7, y = 2","x = 8, y = 2","x = 9, y = 2","x = 10, y = 2","x = 11, y = 2","x = 12, y = 2","x = 13, y = 2","x = 14, y = 2","x = 15, y = 2","x = 16, y = 2","x = 17, y = 2","x = 1, y = 3","x = 2, y = 3","x = 3, y = 3","x = 4, y = 3","x = 5, y = 3","x = 6, y = 3","x = 7, y = 3","x = 8, y = 3","x = 9, y = 3","x = 10, y = 3","x = 11, y = 3","x = 12, y = 3","x = 13, y = 3","x = 14, y = 3","x = 15, y = 3","x = 16, y = 3","x = 17, y = 3","x = 1, y = 4","x = 2, y = 4","x = 3, y = 4","x = 4, y = 4","x = 5, y = 4","x = 6, y = 4","x = 7, y = 4","x = 8, y = 4","x = 9, y = 4","x = 10, y = 4","x = 11, y = 4","x = 12, y = 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|
| b |
| diff -r 000000000000 -r 74fcb3c95a53 test-data/preprocessing_results3.RData |
| b |
| Binary file test-data/preprocessing_results3.RData has changed |
| b |
| diff -r 000000000000 -r 74fcb3c95a53 test-data/preprocessing_results3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/preprocessing_results3.csv Tue Oct 31 15:05:05 2017 -0400 |
| b |
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