| Previous changeset 3:4b5513e25902 (2019-02-28) Next changeset 5:528fb09022be (2019-12-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d |
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modified:
filtering.xml macros.xml test-data/Example_Processed.imzML test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/features_test2.tabular test-data/features_test4.tabular test-data/features_test6.tabular test-data/features_test7.tabular test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata |
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added:
static/images/classification_overview.png |
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| diff -r 4b5513e25902 -r 58376f5a6319 filtering.xml --- a/filtering.xml Thu Feb 28 09:22:46 2019 -0500 +++ b/filtering.xml Fri Mar 22 08:14:21 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.2"> +<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.3"> <description>tool for filtering mass spectrometry imaging data</description> <macros> <import>macros.xml</import> @@ -58,6 +58,9 @@ ## Store features for QC plot featuresinfile = mz(msidata) + all_df = cbind(coord(msidata)[,1:2], rep("removed pixels", times=ncol(msidata))) + colnames(all_df)[3] = "annotation" + ## Next steps will only run if there are more than 0 pixels/features in the file if (ncol(msidata)>0 & nrow(msidata) >0) @@ -138,8 +141,11 @@ ############################# QC data ##################################### ## dataframe for QC of pixel distribution - position_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata))) - colnames(position_df)[3] = "annotation" + + remaining_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata))) + colnames(remaining_df)[3] = "annotation" + position_df = rbind(all_df, remaining_df) + position_df[row.names(unique(position_df[,c("x", "y")])),] position_df\$annotation = factor(position_df\$annotation) gc() @@ -444,8 +450,8 @@ </conditional> <param name="imzml_output" type="select" display = "radio" optional = "False" label="Output format" help= "Choose the output format"> - <option value="imzml_format" selected="True">imzML</option> - <option value="rdata_format">RData</option> + <option value="imzml_format" >imzML</option> + <option value="rdata_format" selected="True" >RData</option> </param> </inputs> @@ -593,7 +599,7 @@ **Output** - MSI data as imzML file or .RData (can be read with the Cardinal package in R) -- pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z +- pdf with heatmap showing the pixels that are removed and kept as well as histograms of kept and removed m/z ]]> |
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| diff -r 4b5513e25902 -r 58376f5a6319 macros.xml --- a/macros.xml Thu Feb 28 09:22:46 2019 -0500 +++ b/macros.xml Fri Mar 22 08:14:21 2019 -0400 |
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| @@ -99,6 +99,7 @@ #if str($processed_cond.processed_file) == "processed": msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") centroided(msidata) = $centroids + iData(msidata) = iData(msidata)[] #else msidata <- readImzML('infile') centroided(msidata) = $centroids @@ -129,14 +130,16 @@ minimumy = min(coord(msidata)[,2]) maximumy = max(coord(msidata)[,2]) ## Range of intensities - minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2) - maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2) + minint = round(min(spectra(msidata), na.rm=TRUE), digits=2) + maxint = round(max(spectra(msidata), na.rm=TRUE), digits=2) ## Number of intensities > 0, for if conditions - npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE) + npeaks= sum(spectra(msidata)>0, na.rm=TRUE) + ## Number of NA in spectra matrix + NAcount = sum(is.na(spectra(msidata))) ## Number of NA in spectra matrix - NAcount = sum(is.na(spectra(msidata)[])) - ## Number of NA in spectra matrix - infcount = sum(is.infinite(spectra(msidata)[])) + infcount = sum(is.infinite(spectra(msidata))) + ## Number of duplicated coordinates + dupl_coord = sum(duplicated(coord(msidata))) properties = c("Number of m/z features", "Range of m/z values", @@ -145,7 +148,8 @@ "Range of y coordinates", "Range of intensities", "Number of NA intensities", - "Number of Inf intensities") + "Number of Inf intensities", + "Number of duplicated coordinates") values = c(paste0(maxfeatures), paste0(minmz, " - ", maxmz), @@ -154,7 +158,8 @@ paste0(minimumy, " - ", maximumy), paste0(minint, " - ", maxint), paste0(NAcount), - paste0(infcount)) + paste0(infcount), + paste0(dupl_coord)) property_df = data.frame(properties, values) ]]></token> @@ -229,7 +234,7 @@ <xml name="reading_msidata"> <param name="infile" type="data" format="imzml,rdata,analyze75" label="MSI data" - help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload)"/> + help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/> <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> <conditional name="processed_cond"> <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file"> |
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| diff -r 4b5513e25902 -r 58376f5a6319 static/images/classification_overview.png |
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| Binary file static/images/classification_overview.png has changed |
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| diff -r 4b5513e25902 -r 58376f5a6319 test-data/Example_Processed.imzML --- a/test-data/Example_Processed.imzML Thu Feb 28 09:22:46 2019 -0500 +++ b/test-data/Example_Processed.imzML Fri Mar 22 08:14:21 2019 -0400 |
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| b'@@ -1,373 +1,380 @@\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="{9D501BDC-5344-4916-B7E9-7E795B02C856}"/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7E8FDB93053915D3EDB51B70AA0619AC209964DF"/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" 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 - p NSI Full ms [100,00-800,00]"/>\r\n- </referenceableParamGroup>\r\n- <referenceableParamGroup id="spectrum1">\r\n- <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>\r\n- <cvParam cvRef="MS" accession'..b' <referenceableParamGroupRef ref="intensityArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="436764"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\n+ <binary />\n+ </binaryDataArray>\n+ </binaryDataArrayList>\n+ </spectrum>\n+ <spectrum id="Scan=8" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="7">\n+ <referenceableParamGroupRef ref="spectrum1"/>\n+ <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="168.27018147522492"/>\n+ <scanList count="1">\n+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>\n+ <scan instrumentConfigurationRef="LTQFTUltra0">\n+ <referenceableParamGroupRef ref="scan1"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>\n+ </scan>\n+ </scanList>\n+ <binaryDataArrayList count="2">\n+ <binaryDataArray encodedLength="0">\n+ <referenceableParamGroupRef ref="mzArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\n+ <binary />\n+ </binaryDataArray>\n+ <binaryDataArray encodedLength="0">\n+ <referenceableParamGroupRef ref="intensityArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="503956"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\n+ <binary />\n+ </binaryDataArray>\n+ </binaryDataArrayList>\n+ </spectrum>\n+ <spectrum id="Scan=9" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="8">\n+ <referenceableParamGroupRef ref="spectrum1"/>\n+ <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="243.5395066031077"/>\n+ <scanList count="1">\n+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>\n+ <scan instrumentConfigurationRef="LTQFTUltra0">\n+ <referenceableParamGroupRef ref="scan1"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>\n+ </scan>\n+ </scanList>\n+ <binaryDataArrayList count="2">\n+ <binaryDataArray encodedLength="0">\n+ <referenceableParamGroupRef ref="mzArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\n+ <binary />\n+ </binaryDataArray>\n+ <binaryDataArray encodedLength="0">\n+ <referenceableParamGroupRef ref="intensityArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\n+ <binary />\n+ </binaryDataArray>\n+ </binaryDataArrayList>\n+ </spectrum>\n+ </spectrumList>\n+ </run>\n+</mzML>\n' |
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| diff -r 4b5513e25902 -r 58376f5a6319 test-data/features_test2.tabular --- a/test-data/features_test2.tabular Thu Feb 28 09:22:46 2019 -0500 +++ b/test-data/features_test2.tabular Fri Mar 22 08:14:21 2019 -0400 |
| b |
| b'@@ -99,3 +99,8057 @@\n 946.450012207031\t2\tA\t0.003494\t0.042887\t0.032578\n 979.395385742188\t2\tC\t0.003494\t-0.009858\t-0.008482\n 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|
| b |
| diff -r 4b5513e25902 -r 58376f5a6319 test-data/features_test4.tabular --- a/test-data/features_test4.tabular Thu Feb 28 09:22:46 2019 -0500 +++ b/test-data/features_test4.tabular Fri Mar 22 08:14:21 2019 -0400 |
| b |
| b'@@ -99,3 +99,8057 @@\n 927.295166015625\t3\tA\t0.00081\t0.03242\t0.019578\n 957.467712402344\t3\tA\t0.000805\t0.034961\t0.029421\n 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|
| b |
| diff -r 4b5513e25902 -r 58376f5a6319 test-data/features_test6.tabular --- a/test-data/features_test6.tabular Thu Feb 28 09:22:46 2019 -0500 +++ b/test-data/features_test6.tabular Fri Mar 22 08:14:21 2019 -0400 |
| b |
| b'@@ -19,3 +19,8137 @@\n 900.434692382812\t2\t3\t2\tA\t30.041667\t0\t1\t1\n 900.470520019531\t2\t3\t2\tA\t19.166667\t0\t1\t1\n 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|
| b |
| diff -r 4b5513e25902 -r 58376f5a6319 test-data/features_test7.tabular --- a/test-data/features_test7.tabular Thu Feb 28 09:22:46 2019 -0500 +++ b/test-data/features_test7.tabular Fri Mar 22 08:14:21 2019 -0400 |
| b |
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