| Next changeset 1:845fee459824 (2018-03-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd |
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added:
msi_ion_images.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/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_rdata.pdf test-data/LM8_file16.rdata test-data/inputpeptides.csv test-data/inputpeptides.txt test-data/preprocessing_results1.RData |
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| b'@@ -0,0 +1,263 @@\n+<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.7.0">\n+ <description>\n+ mass spectrometry imaging heatmaps\n+ </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+ <requirement type="package" version="2.23-15">r-kernsmooth</requirement>\n+ <requirement type="package" version="0.20-35">r-lattice</requirement>\n+ </requirements>\n+ <command detect_errors="aggressive">\n+<![CDATA[\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_heatmaps}\' &&\n+ Rscript \'${MSI_heatmaps}\'\n+]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="MSI_heatmaps"><![CDATA[\n+################################# load libraries and read file #########################\n+\n+library(Cardinal)\n+library(gridExtra)\n+library(KernSmooth)\n+library(lattice)\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+#if $massfile:\n+ ### Read tabular file with peptide masses for plots and heatmap images: \n+ input_list = read.delim("$massfile", header = FALSE, na.strings=c("","NA", "#NUM!", "#ZAHL!"), stringsAsFactors = FALSE)\n+ if (ncol(input_list) == 1)\n+ {\n+ input_list = cbind(input_list, input_list)\n+ }\n+#else\n+ input_list = data.frame(0, 0)\n+#end if\n+colnames(input_list)[1:2] = c("mz", "name")\n+\n+###################################### file properties in numbers ######################\n+\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+## Range of intensities\n+minint = round(min(spectra(msidata)[]), digits=2)\n+maxint = round(max(spectra(msidata)[]), digits=2)\n+medint = round(median(spectra(msidata)[]), digits=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+\n+## Processing informations\n+processinginfo = processingData(msidata)\n+centroidedinfo = processinginfo@centroided # TRUE or FALSE\n+\n+## if TRUE write processinginfo if no write FALSE\n+\n+## normalization\n+if (length(processinginfo@normalization) == 0) {\n+ normalizationinfo=\'FALSE\'\n+} else {\n+ normalizationinfo=processinginfo@normalization\n+}\n+## smoothing\n+if (length(processinginfo@smoothing) == 0) {\n+ smoothinginfo=\'FALSE\'\n+} else {\n+ smoothinginfo=processinginfo@smoothing\n+}\n+## baseline\n+if (length(processinginfo@baselineReduction) == 0) {\n+ baselinereductioninfo=\'FALSE\'\n+} else {\n+ baselinereductioninfo=processinginfo@baselineReduction\n+}\n+## peak picking\n+if (length(processinginfo@peakPicking) == 0) {\n+ peakpickinginfo=\'FALSE\'\n+} else {\n+ peakpickinginfo=processinginfo@peakPicking\n+}\n+\n+### calculate how many input masses are valid: \n+i'..b'alton, contrast.enhance = "histogram", \n+ main= paste0(mass, ") ", inputnames[mass], " (", round(inputmz[mass], digits = 2)," \xc2\xb1 ", $plusminusinDalton, " Da)")))\n+ }\n+ } else {print("The input masses were outside the mass range")}\n+\n+ dev.off()\n+\n+}else{\n+ print("inputfile has no intensities > 0")\n+dev.off()\n+}\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"\n+ help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>\n+ <param name="filename" type="text" value="" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name."/>\n+ <param name="massfile" type="data" optional="true" format="tabular" label="Text file with masses and names"\n+ help="first column mass (m/z), second column mass name, tab separated file"/>\n+ <param name="plusminusinDalton" value="0.25" type="float" label="Mass range" help="plusminus mass window in Dalton"/>\n+ </inputs>\n+ <outputs>\n+ <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label = "${tool.name} on $infile.display_name"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="infile" value="" ftype="imzml">\n+ <composite_data value="Example_Continuous.imzML"/>\n+ <composite_data value="Example_Continuous.ibd"/>\n+ </param>\n+ <param name="massfile" value="inputpeptides.csv" ftype="tabular"/>\n+ <param name="plusminusinDalton" value="0.25"/>\n+ <param name="filename" value="Testfile_imzml"/>\n+ <output name="plots" file="Heatmaps_imzml.pdf" compare="sim_size" delta="20000"/>\n+ </test>\n+\n+ <test>\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="massfile" value="inputpeptides.txt" ftype="tabular"/>\n+ <param name="plusminusinDalton" value="0.5"/>\n+ <param name="filename" value="Testfile_analyze75"/>\n+ <output name="plots" file="Heatmaps_analyze75.pdf" compare="sim_size" delta="20000"/>\n+ </test>\n+ <test>\n+ <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>\n+ <param name="massfile" value="inputpeptides.csv" ftype="tabular"/>\n+ <param name="plusminusinDalton" value="0.1"/>\n+ <param name="filename" value="Testfile_rdata"/>\n+ <output name="plots" file="Heatmaps_rdata.pdf" compare="sim_size" delta="20000"/>\n+ </test>\n+ <test>\n+ <param name="infile" value="LM8_file16.rdata" ftype="rdata"/>\n+ <param name="massfile" value="inputpeptides.txt" ftype="tabular"/>\n+ <param name="plusminusinDalton" value="0.1"/>\n+ <param name="filename" value="Testfile_rdata"/>\n+ <output name="plots" file="Heatmaps_LM8_file16.pdf" compare="sim_size" delta="20000"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+Heatmaps for different ion masses in mass-spectrometry imaging data. \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 contains heatmaps for every ion mass of interest as pdf. \n+\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 385e8a4accd9 test-data/Example_Continuous.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Example_Continuous.imzML Mon Nov 27 13:49:35 2017 -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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| diff -r 000000000000 -r 385e8a4accd9 test-data/inputpeptides.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides.csv Mon Nov 27 13:49:35 2017 -0500 |
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| @@ -0,0 +1,3 @@ +152 mass1 +328.9 mass2 +185.2 mass3 |
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| diff -r 000000000000 -r 385e8a4accd9 test-data/inputpeptides.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides.txt Mon Nov 27 13:49:35 2017 -0500 |
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