Mercurial > repos > galaxyp > msi_qualitycontrol
changeset 8:52ef77866de8 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
| author | galaxyp |
|---|---|
| date | Mon, 28 May 2018 12:38:50 -0400 |
| parents | b86a66dd1a16 |
| children | 963c7ec00141 |
| files | msi_qualitycontrol.xml test-data/Analyze75.hdr test-data/Analyze75.img test-data/Analyze75.t2m test-data/LM8_file16.rdata test-data/LM8_file16output.pdf test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/Testfile_qualitycontrol_analyze75.pdf test-data/Testfile_qualitycontrol_imzml.pdf test-data/Testfile_qualitycontrol_rdata.pdf test-data/empty_spectra.rdata test-data/example_continousS042.RData test-data/inputcalibrantfile2.txt test-data/inputpeptides.csv test-data/inputpeptides.txt test-data/preprocessed.RData test-data/preprocessing_results1.RData |
| diffstat | 20 files changed, 54 insertions(+), 46 deletions(-) [+] |
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--- a/msi_qualitycontrol.xml Tue May 08 02:36:43 2018 -0400 +++ b/msi_qualitycontrol.xml Mon May 28 12:38:50 2018 -0400 @@ -1,9 +1,9 @@ -<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.7.0.5"> +<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.0"> <description> mass spectrometry imaging QC </description> <requirements> - <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement> + <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> <requirement type="package" version="2.2.1">r-ggplot2</requirement> <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> <requirement type="package" version="2.2.1">r-gridextra</requirement> @@ -12,12 +12,12 @@ <command detect_errors="exit_code"> <![CDATA[ #if $infile.ext == 'imzml' - cp '${infile.extra_files_path}/imzml' infile.imzML && - cp '${infile.extra_files_path}/ibd' infile.ibd && + ln -s '${infile.extra_files_path}/imzml' infile.imzML && + ln -s '${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 && + ln -s '${infile.extra_files_path}/hdr' infile.hdr && + ln -s '${infile.extra_files_path}/img' infile.img && + ln -s '${infile.extra_files_path}/t2m' infile.t2m && #else ln -s '$infile' infile.RData && #end if @@ -37,10 +37,9 @@ ## Read MALDI Imaging dataset #if $infile.ext == 'imzml' - msidata = readMSIData('infile.imzML') + msidata = readImzML('infile') #elif $infile.ext == 'analyze75' - msidata = readMSIData('infile.hdr') - + msidata = readAnalyze('infile') #else load('infile.RData') #end if @@ -107,7 +106,7 @@ peakpickinginfo=processinginfo@peakPicking } -### Read tabular file with peptide masses for plots and heatmap images: +### Read tabular file with masses for plots and heatmap images: #if $peptide_file: @@ -143,10 +142,8 @@ number_calibrants_in = length(calibrant_list[,1]) number_calibrants_valid = length(inputcalibrants[,1]) #else - ###inputcalibrants = data.frame(0,0) inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2)) - number_calibrants_in = 0 number_calibrants_valid = 0 #end if @@ -372,7 +369,7 @@ { image(msidata, mz=inputmasses[mass], plusminus=$plusminus_dalton, main= paste0(inputnames[mass], " (", round(inputmasses[mass], digits = 2)," ± ", $plusminus_dalton, " Da)"), - contrast.enhance = "histogram", ylim=c(maximumy+2, 0)) + contrast.enhance = "histogram", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy)) } } else {print("3) The inputpeptide masses were not provided or outside the mass range")} @@ -428,7 +425,7 @@ pca = PCA(msidata, ncomp=2) par(mfrow = c(2,1)) plot(pca, col=c("black", "darkgrey"), main="PCA for two components") - image(pca, col=c("black", "white"),ylim=c(maximumy+2, 0), strip=FALSE) + image(pca, col=c("black", "white"),ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), strip=FALSE) ############################# III) properties over acquisition (spectra index)########## @@ -600,12 +597,12 @@ <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="" optional="true" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name."/> - <param name="peptide_file" type="data" optional="true" format="tabular" label="Text file with peptidemasses and names" - help="first column peptide m/z, second column peptide name, tab separated file"/> + <param name="peptide_file" type="data" optional="true" format="tabular" label="Text file with masses and names" + help="first column m/z, second column name, tab separated file"/> <param name="calibrant_file" type="data" optional="true" format="tabular" - label="Internal calibrants" + label="Internal calibrants and names" help="Used for plot number of calibrant per spectrum and for zoomed in mass spectra"/> - <param name="plusminus_dalton" value="0.25" type="text" label="Mass range" help="plusminus mass window in Dalton"/> + <param name="plusminus_dalton" value="0.25" type="text" label="Mass range in Dalton" help="Plusminus mass window in Dalton for calibrant and peptide plots"/> <repeat name="calibrantratio" title="Plot fold change of two masses for each spectrum" min="0" max="10"> <param name="mass1" value="1111" type="float" label="Mass 1" help="First mass in Dalton"/> <param name="mass2" value="2222" type="float" label="Mass 2" help="Second mass in Dalton"/> @@ -623,8 +620,8 @@ <composite_data value="Example_Continuous.imzML" /> <composite_data value="Example_Continuous.ibd" /> </param> - <param name="peptide_file" value="inputpeptides.csv" ftype="csv"/> - <param name="calibrant_file" ftype="txt" value="inputcalibrantfile1.txt"/> + <param name="peptide_file" value="inputpeptides.txt"/> + <param name="calibrant_file" value="inputcalibrantfile1.txt"/> <param name="plusminus_dalton" value="0.25"/> <param name="filename" value="Testfile_imzml"/> <repeat name="calibrantratio"> @@ -633,49 +630,60 @@ <param name="distance" value="0.25"/> <param name="filenameratioplot" value = "Ratio of mass1 (111) / mass2 (222)"/> </repeat> - <output name="plots" file="Testfile_qualitycontrol_imzml.pdf" compare="sim_size" delta="20000"/> + <output name="plots" file="QC_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="peptide_file" value="inputpeptides.txt" ftype="txt"/> - <param name="calibrant_file" ftype="txt" value="inputcalibrantfile2.txt"/> + <param name="peptide_file" value="inputpeptides.txt"/> + <param name="calibrant_file" value="inputcalibrantfile2.txt"/> <param name="plusminus_dalton" value="0.5"/> <param name="filename" value="Testfile_analyze75"/> - <output name="plots" file="Testfile_qualitycontrol_analyze75.pdf" compare="sim_size" delta="20000"/> + <output name="plots" file="QC_analyze75.pdf" compare="sim_size" delta="20000"/> </test> - <test> - <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/> + <param name="infile" value="preprocessed.RData" ftype="rdata"/> + <param name="plusminus_dalton" value="0"/> + <param name="filename" value="Testfile_rdata"/> + <output name="plots" file="QC_rdata.pdf" compare="sim_size" delta="20000"/> + </test> + <test> + <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> + <param name="peptide_file" value="inputpeptides.txt"/> + <param name="calibrant_file" value="inputcalibrantfile2.txt"/> <param name="plusminus_dalton" value="0.1"/> <param name="filename" value="Testfile_rdata"/> - <output name="plots" file="Testfile_qualitycontrol_rdata.pdf" compare="sim_size" delta="20000"/> - </test> - <test> - <param name="infile" value="LM8_file16.rdata" ftype="rdata"/> - <param name="peptide_file" value="inputpeptides.txt" ftype="txt"/> - <param name="calibrant_file" ftype="txt" value="inputcalibrantfile2.txt"/> - <param name="plusminus_dalton" value="0.1"/> - <param name="filename" value="Testfile_rdata"/> - <output name="plots" file="LM8_file16output.pdf" compare="sim_size" delta="20000"/> + <output name="plots" file="QC_empty_spectra.pdf" compare="sim_size" delta="20000"/> </test> </tests> <help> <![CDATA[ -Quality control for maldi imaging mass spectrometry data. The output of this tool contains key values and plots of the imaging data as pdf. -For additional beautiful heatmap images use the MSI ion images tool and to plot more mass spectra use the MSI massspectra tool. +Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_ + +This tool uses some Cardinal functions to create a quality control report with descriptive plots for 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/>`_ +- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData) +Options: +- masses of interest as tabular file, used to generate heatmap images +- internal calibrants as tabular file, used for the following plots: Number of calibrant per spectrum, heatmap images, mass-spectrum plot zoomed in for calibrant region, ppm accuracy +- fold change plot: draws a heatmap of the fold change of two masses (log2(intensity ratio)) + +Output: + +- pdf with numbers and descriptive plots to check the quality of the mass-spectrometry imaging data + +Tip: + +- For additional heatmap images use the MSI ion images tool and to plot more mass spectra use the MSI massspectra tool. ]]> </help>
--- a/test-data/inputcalibrantfile2.txt Tue May 08 02:36:43 2018 -0400 +++ b/test-data/inputcalibrantfile2.txt Mon May 28 12:38:50 2018 -0400 @@ -1,3 +1,3 @@ 869.51 mass1 -1001.62 mass2 -1023.6 mass3 +1111.1 mass2 +1296.7 mass3
--- a/test-data/inputpeptides.csv Tue May 08 02:36:43 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -152 mass1 -328.9 mass2 -185.2 mass3