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changeset 0:385e8a4accd9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
author galaxyp
date Mon, 27 Nov 2017 13:49:35 -0500
parents
children 845fee459824
files 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
diffstat 14 files changed, 642 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msi_ion_images.xml	Mon Nov 27 13:49:35 2017 -0500
@@ -0,0 +1,263 @@
+<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.7.0">
+    <description>
+        mass spectrometry imaging heatmaps
+    </description>
+    <requirements>
+        <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>
+        <requirement type="package" version="2.2.1">r-gridextra</requirement>
+        <requirement type="package" version="2.23-15">r-kernsmooth</requirement>
+        <requirement type="package" version="0.20-35">r-lattice</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+<![CDATA[
+        #if $infile.ext == 'imzml'
+            cp '${infile.extra_files_path}/imzml' infile.imzML &&
+            cp '${infile.extra_files_path}/ibd' infile.ibd &&
+        #elif $infile.ext == 'analyze75'
+            cp '${infile.extra_files_path}/hdr' infile.hdr &&
+            cp '${infile.extra_files_path}/img' infile.img &&
+            cp '${infile.extra_files_path}/t2m' infile.t2m &&
+        #else
+            ln -s $infile infile.RData &&
+        #end if
+        cat '${MSI_heatmaps}' &&
+        Rscript '${MSI_heatmaps}'
+]]>
+    </command>
+    <configfiles>
+        <configfile name="MSI_heatmaps"><![CDATA[
+################################# load libraries and read file #########################
+
+library(Cardinal)
+library(gridExtra)
+library(KernSmooth)
+library(lattice)
+
+## Read MALDI Imaging dataset
+
+#if $infile.ext == 'imzml'
+    msidata <- readMSIData('infile.imzML')
+#elif $infile.ext == 'analyze75'
+    msidata <- readMSIData('infile.hdr')
+#else
+    load('infile.RData')
+#end if
+
+#if $massfile:
+    ### Read tabular file with peptide masses for plots and heatmap images: 
+    input_list = read.delim("$massfile", header = FALSE, na.strings=c("","NA", "#NUM!", "#ZAHL!"), stringsAsFactors = FALSE)
+        if (ncol(input_list) == 1)
+        {
+            input_list = cbind(input_list, input_list)
+        }
+#else
+    input_list = data.frame(0, 0)
+#end if
+colnames(input_list)[1:2] = c("mz", "name")
+
+###################################### file properties in numbers ######################
+
+## Number of features (mz)
+maxfeatures = length(features(msidata))
+## Range mz
+minmz = round(min(mz(msidata)), digits=2)
+maxmz = round(max(mz(msidata)), digits=2)
+## Number of spectra (pixels)
+pixelcount = length(pixels(msidata))
+## Range x coordinates
+minimumx = min(coord(msidata)[,1])
+maximumx = max(coord(msidata)[,1])
+## Range y coordinates
+minimumy = min(coord(msidata)[,2])
+maximumy = max(coord(msidata)[,2])
+## Range of intensities
+minint = round(min(spectra(msidata)[]), digits=2)
+maxint = round(max(spectra(msidata)[]), digits=2)
+medint = round(median(spectra(msidata)[]), digits=2)
+## Number of intensities > 0
+npeaks= sum(spectra(msidata)[]>0)
+## Spectra multiplied with mz (potential number of peaks)
+numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
+## Percentage of intensities > 0
+percpeaks = round(npeaks/numpeaks*100, digits=2)
+## Number of empty TICs
+TICs = colSums(spectra(msidata)[]) 
+NumemptyTIC = sum(TICs == 0)
+
+## Processing informations
+processinginfo = processingData(msidata)
+centroidedinfo = processinginfo@centroided # TRUE or FALSE
+
+## if TRUE write processinginfo if no write FALSE
+
+## normalization
+if (length(processinginfo@normalization) == 0) {
+  normalizationinfo='FALSE'
+} else {
+  normalizationinfo=processinginfo@normalization
+}
+## smoothing
+if (length(processinginfo@smoothing) == 0) {
+  smoothinginfo='FALSE'
+} else {
+  smoothinginfo=processinginfo@smoothing
+}
+## baseline
+if (length(processinginfo@baselineReduction) == 0) {
+  baselinereductioninfo='FALSE'
+} else {
+  baselinereductioninfo=processinginfo@baselineReduction
+}
+## peak picking
+if (length(processinginfo@peakPicking) == 0) {
+  peakpickinginfo='FALSE'
+} else {
+  peakpickinginfo=processinginfo@peakPicking
+}
+
+### calculate how many input masses are valid: 
+inputmasses = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]
+
+inputmz = inputmasses[,1]
+inputnames = inputmasses[,2]
+
+properties = c("Number of mz features",
+               "Range of mz values [Da]",
+               "Number of pixels", 
+               "Range of x coordinates", 
+               "Range of y coordinates",
+               "Range of intensities", 
+               "Median of intensities",
+               "Intensities > 0",
+               "Number of zero TICs",
+               "Preprocessing", 
+               "Normalization", 
+               "Smoothing",
+               "Baseline reduction",
+               "Peak picking",
+               "Centroided", 
+                paste0("# valid masses in ", "$filename"))
+
+values = c(paste0(maxfeatures), 
+           paste0(minmz, " - ", maxmz), 
+           paste0(pixelcount), 
+           paste0(minimumx, " - ", maximumx),  
+           paste0(minimumy, " - ", maximumy), 
+           paste0(minint, " - ", maxint), 
+           paste0(medint),
+           paste0(percpeaks, " %"), 
+           paste0(NumemptyTIC), 
+           paste0(" "),
+           paste0(normalizationinfo),
+           paste0(smoothinginfo),
+           paste0(baselinereductioninfo),
+           paste0(peakpickinginfo),
+           paste0(centroidedinfo), 
+           paste0(length(inputmz), "/", length(input_list[,1])))
+
+property_df = data.frame(properties, values)
+
+######################################## PDF #############################################
+##########################################################################################
+##########################################################################################
+
+
+pdf("heatmaps.pdf", fonts = "Times", pointsize = 12)
+plot(0,type='n',axes=FALSE,ann=FALSE)
+#if not $filename:
+    #set $filename = $infile.display_name
+#end if
+title(main=paste("Quality control of MSI data\n\n", "Filename:", "$filename"))
+
+############################# I) numbers ####################################
+#############################################################################
+
+grid.table(property_df, rows= NULL)
+
+if (npeaks > 0)
+{
+    if (length(inputmz) != 0)
+    {
+      for (mass in 1:length(inputmz))
+      {
+        print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),
+              lattice=TRUE, ylim = c(maximumy+1,minimumy-1), plusminus = $plusminusinDalton, contrast.enhance = "histogram", 
+              main= paste0(mass, ") ", inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminusinDalton, " Da)")))
+      }
+    } else {print("The input masses were outside the mass range")}
+
+    dev.off()
+
+}else{
+  print("inputfile has no intensities > 0")
+dev.off()
+}
+    ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
+            help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
+        <param name="filename" type="text" value="" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name."/>
+        <param name="massfile" type="data" optional="true" format="tabular" label="Text file with masses and names"
+            help="first column mass (m/z), second column mass name, tab separated file"/>
+        <param name="plusminusinDalton" value="0.25" type="float" label="Mass range" help="plusminus mass window in Dalton"/>
+    </inputs>
+    <outputs>
+        <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label = "${tool.name} on $infile.display_name"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="" ftype="imzml">
+                <composite_data value="Example_Continuous.imzML"/>
+                <composite_data value="Example_Continuous.ibd"/>
+            </param>
+            <param name="massfile" value="inputpeptides.csv" ftype="tabular"/>
+            <param name="plusminusinDalton" value="0.25"/>
+            <param name="filename" value="Testfile_imzml"/>
+            <output name="plots" file="Heatmaps_imzml.pdf" compare="sim_size" delta="20000"/>
+        </test>
+
+        <test>
+            <param name="infile" value="" ftype="analyze75">
+                <composite_data value="Analyze75.hdr"/>
+                <composite_data value="Analyze75.img"/>
+                <composite_data value="Analyze75.t2m"/>
+            </param>
+            <param name="massfile" value="inputpeptides.txt" ftype="tabular"/>
+            <param name="plusminusinDalton" value="0.5"/>
+            <param name="filename" value="Testfile_analyze75"/>
+            <output name="plots" file="Heatmaps_analyze75.pdf" compare="sim_size" delta="20000"/>
+        </test>
+        <test>
+            <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>
+            <param name="massfile" value="inputpeptides.csv" ftype="tabular"/>
+            <param name="plusminusinDalton" value="0.1"/>
+            <param name="filename" value="Testfile_rdata"/>
+            <output name="plots" file="Heatmaps_rdata.pdf" compare="sim_size" delta="20000"/>
+        </test>
+        <test>
+            <param name="infile" value="LM8_file16.rdata" ftype="rdata"/>
+            <param name="massfile" value="inputpeptides.txt" ftype="tabular"/>
+            <param name="plusminusinDalton" value="0.1"/>
+            <param name="filename" value="Testfile_rdata"/>
+            <output name="plots" file="Heatmaps_LM8_file16.pdf" compare="sim_size" delta="20000"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Heatmaps for different ion masses in mass-spectrometry imaging data. 
+
+Input data: 3 types of input data can be used:
+
+- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_
+- Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
+- Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
+
+The output of this tool contains heatmaps for every ion mass of interest as pdf. 
+
+    ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btv146</citation>
+    </citations>
+</tool>
Binary file test-data/Analyze75.hdr has changed
Binary file test-data/Analyze75.img has changed
Binary file test-data/Analyze75.t2m has changed
Binary file test-data/Example_Continuous.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Example_Continuous.imzML	Mon Nov 27 13:49:35 2017 -0500
@@ -0,0 +1,373 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<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">
+  <cvList count="3">
+    <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo"/>
+    <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
+    <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>
+  </cvList>
+  <fileDescription>
+    <fileContent>
+      <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
+      <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>
+      <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{554A27FA-79D2-4766-9A2C-862E6D78B1F3}"/>
+      <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="A5BE532D25997B71BE6D20C76561DDC4D5307DDD"/>
+      <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value=""/>
+    </fileContent>
+    <sourceFileList count="1">
+      <sourceFile id="sf1" name="Example.raw" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\">
+        <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW file" value=""/>
+        <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
+        <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>
+      </sourceFile>
+    </sourceFileList>
+    <contact>
+      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>
+      <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institut für Anorganische und Analytische Chemie"/>
+      <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstraße 60, Haus 16, Gießen, Germany"/>
+      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>
+    </contact>
+  </fileDescription>
+  <referenceableParamGroupList count="4">
+    <referenceableParamGroup id="mzArray">
+      <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
+      <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+      <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
+      <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="intensityArray">
+      <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
+      <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
+      <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
+      <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="scan1">
+      <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value=""/>
+      <cvParam cvRef="MS" accession="MS:1000095" name="linear" value=""/>
+      <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="spectrum1">
+      <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
+      <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
+      <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>
+      <cvParam cvRef="MS" accession="MS:1000129" name="negative scan" value=""/>
+    </referenceableParamGroup>
+  </referenceableParamGroupList>
+  <sampleList count="1">
+    <sample id="sample1" name="Sample1">
+      <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/>
+    </sample>
+  </sampleList>
+  <softwareList count="2">
+    <software id="Xcalibur" version="2.2">
+      <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
+    </software>
+    <software id="TMC" version="1.1 beta">
+      <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value=""/>
+    </software>
+  </softwareList>
+  <scanSettingsList count="1">
+    <scanSettings id="scansettings1">
+      <cvParam cvRef="IMS" accession="IMS:1000401" name="top down" value=""/>
+      <cvParam cvRef="IMS" accession="IMS:1000413" name="flyback" value=""/>
+      <cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan" value=""/>
+      <cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right" value=""/>
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+      <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>
+      <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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+      <cvParam cvRef="MS" accession="MS:1000835" name="matrix solution concentration" value="10"/>
+      <cvParam cvRef="MS" accession="MS:1000834" name="matrix solution" value="DHB"/>
+    </scanSettings>
+  </scanSettingsList>
+  <instrumentConfigurationList count="1">
+    <instrumentConfiguration id="LTQFTUltra0">
+      <cvParam cvRef="MS" accession="MS:1000557" name="LTQ FT Ultra" value=""/>
+      <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="none"/>
+      <componentList count="3">
+        <source order="1">
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+          <cvParam cvRef="IMS" accession="IMS:1000202" name="target material" value="Conductive Glas"/>
+        </source>
+        <analyzer order="2">
+          <cvParam cvRef="MS" accession="MS:1000264" name="ion trap" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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+          <cvParam cvRef="MS" accession="MS:1000120" name="transient recorder" value=""/>
+        </detector>
+      </componentList>
+      <softwareRef ref="Xcalibur"/>
+    </instrumentConfiguration>
+  </instrumentConfigurationList>
+  <dataProcessingList count="2">
+    <dataProcessing id="XcaliburProcessing">
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+      </processingMethod>
+    </dataProcessing>
+    <dataProcessing id="TMCConversion">
+      <processingMethod order="2" softwareRef="TMC">
+        <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+      </processingMethod>
+    </dataProcessing>
+  </dataProcessingList>
+  <run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44">
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\ No newline at end of file
Binary file test-data/Heatmaps_LM8_file16.pdf has changed
Binary file test-data/Heatmaps_analyze75.pdf has changed
Binary file test-data/Heatmaps_imzml.pdf has changed
Binary file test-data/Heatmaps_rdata.pdf has changed
Binary file test-data/LM8_file16.rdata has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides.csv	Mon Nov 27 13:49:35 2017 -0500
@@ -0,0 +1,3 @@
+152	mass1
+328.9	mass2
+185.2	mass3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides.txt	Mon Nov 27 13:49:35 2017 -0500
@@ -0,0 +1,3 @@
+854.5
+1296.7
+2000.8
Binary file test-data/preprocessing_results1.RData has changed