| Previous changeset 7:b86a66dd1a16 (2018-05-08) Next changeset 9:963c7ec00141 (2018-06-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 |
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modified:
msi_qualitycontrol.xml test-data/Analyze75.hdr test-data/Analyze75.img test-data/Analyze75.t2m test-data/inputcalibrantfile2.txt test-data/inputpeptides.txt |
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added:
test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/empty_spectra.rdata test-data/preprocessed.RData |
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removed:
test-data/LM8_file16.rdata test-data/LM8_file16output.pdf test-data/Testfile_qualitycontrol_analyze75.pdf test-data/Testfile_qualitycontrol_imzml.pdf test-data/Testfile_qualitycontrol_rdata.pdf test-data/example_continousS042.RData test-data/inputpeptides.csv test-data/preprocessing_results1.RData |
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| diff -r b86a66dd1a16 -r 52ef77866de8 msi_qualitycontrol.xml --- a/msi_qualitycontrol.xml Tue May 08 02:36:43 2018 -0400 +++ b/msi_qualitycontrol.xml Mon May 28 12:38:50 2018 -0400 |
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| b'@@ -1,9 +1,9 @@\n-<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.7.0.5">\n+<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.0">\n <description>\n mass spectrometry imaging QC\n </description>\n <requirements>\n- <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>\n+ <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>\n <requirement type="package" version="2.2.1">r-ggplot2</requirement>\n <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>\n <requirement type="package" version="2.2.1">r-gridextra</requirement>\n@@ -12,12 +12,12 @@\n <command detect_errors="exit_code">\n <![CDATA[\n #if $infile.ext == \'imzml\'\n- cp \'${infile.extra_files_path}/imzml\' infile.imzML &&\n- cp \'${infile.extra_files_path}/ibd\' infile.ibd &&\n+ ln -s \'${infile.extra_files_path}/imzml\' infile.imzML &&\n+ ln -s \'${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+ ln -s \'${infile.extra_files_path}/hdr\' infile.hdr &&\n+ ln -s \'${infile.extra_files_path}/img\' infile.img &&\n+ ln -s \'${infile.extra_files_path}/t2m\' infile.t2m &&\n #else\n ln -s \'$infile\' infile.RData &&\n #end if\n@@ -37,10 +37,9 @@\n ## Read MALDI Imaging dataset\n \n #if $infile.ext == \'imzml\'\n- msidata = readMSIData(\'infile.imzML\')\n+ msidata = readImzML(\'infile\')\n #elif $infile.ext == \'analyze75\'\n- msidata = readMSIData(\'infile.hdr\')\n-\n+ msidata = readAnalyze(\'infile\')\n #else\n load(\'infile.RData\')\n #end if\n@@ -107,7 +106,7 @@\n peakpickinginfo=processinginfo@peakPicking\n }\n \n-### Read tabular file with peptide masses for plots and heatmap images: \n+### Read tabular file with masses for plots and heatmap images: \n \n #if $peptide_file:\n \n@@ -143,10 +142,8 @@\n number_calibrants_in = length(calibrant_list[,1])\n number_calibrants_valid = length(inputcalibrants[,1])\n #else\n- ###inputcalibrants = data.frame(0,0)\n \n inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2))\n-\n number_calibrants_in = 0\n number_calibrants_valid = 0\n #end if\n@@ -372,7 +369,7 @@\n {\n image(msidata, mz=inputmasses[mass], plusminus=$plusminus_dalton, \n main= paste0(inputnames[mass], " (", round(inputmasses[mass], digits = 2)," \xc2\xb1 ", $plusminus_dalton, " Da)"),\n- contrast.enhance = "histogram", ylim=c(maximumy+2, 0))\n+ contrast.enhance = "histogram", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy))\n }\n } else {print("3) The inputpeptide masses were not provided or outside the mass range")}\n \n@@ -428,7 +425,7 @@\n pca = PCA(msidata, ncomp=2) \n par(mfrow = c(2,1))\n plot(pca, col=c("black", "darkgrey"), main="PCA for two components")\n- image(pca, col=c("black", "white"),ylim=c(maximumy+2, 0), strip=FALSE)\n+ image(pca, col=c("black", "white"),ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), strip=FALSE)\n \n \n ############################# III) properties over acquisition (spectra index)##########\n@@ -600,12 +597,12 @@\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="" optional="true" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name."/>\n- <param name="peptide_file" type="data" optional="true" format="tabular" label="Text '..b'75.img"/>\n <composite_data value="Analyze75.t2m"/>\n </param>\n- <param name="peptide_file" value="inputpeptides.txt" ftype="txt"/>\n- <param name="calibrant_file" ftype="txt" value="inputcalibrantfile2.txt"/>\n+ <param name="peptide_file" value="inputpeptides.txt"/>\n+ <param name="calibrant_file" value="inputcalibrantfile2.txt"/>\n <param name="plusminus_dalton" value="0.5"/>\n <param name="filename" value="Testfile_analyze75"/>\n- <output name="plots" file="Testfile_qualitycontrol_analyze75.pdf" compare="sim_size" delta="20000"/>\n+ <output name="plots" file="QC_analyze75.pdf" compare="sim_size" delta="20000"/>\n </test>\n-\n <test>\n- <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>\n+ <param name="infile" value="preprocessed.RData" ftype="rdata"/>\n+ <param name="plusminus_dalton" value="0"/>\n+ <param name="filename" value="Testfile_rdata"/>\n+ <output name="plots" file="QC_rdata.pdf" compare="sim_size" delta="20000"/>\n+ </test>\n+ <test>\n+ <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>\n+ <param name="peptide_file" value="inputpeptides.txt"/>\n+ <param name="calibrant_file" value="inputcalibrantfile2.txt"/>\n <param name="plusminus_dalton" value="0.1"/>\n <param name="filename" value="Testfile_rdata"/>\n- <output name="plots" file="Testfile_qualitycontrol_rdata.pdf" compare="sim_size" delta="20000"/>\n- </test>\n- <test>\n- <param name="infile" value="LM8_file16.rdata" ftype="rdata"/>\n- <param name="peptide_file" value="inputpeptides.txt" ftype="txt"/>\n- <param name="calibrant_file" ftype="txt" value="inputcalibrantfile2.txt"/>\n- <param name="plusminus_dalton" value="0.1"/>\n- <param name="filename" value="Testfile_rdata"/>\n- <output name="plots" file="LM8_file16output.pdf" compare="sim_size" delta="20000"/>\n+ <output name="plots" file="QC_empty_spectra.pdf" compare="sim_size" delta="20000"/>\n </test>\n </tests>\n <help>\n <![CDATA[\n-Quality control for maldi imaging mass spectrometry data. The output of this tool contains key values and plots of the imaging data as pdf. \n-For additional beautiful heatmap images use the MSI ion images tool and to plot more mass spectra use the MSI massspectra tool. \n+Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_\n+\n+This tool uses some Cardinal functions to create a quality control report with descriptive plots for 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+- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_\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+Options: \n \n+- masses of interest as tabular file, used to generate heatmap images\n+- 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\n+- fold change plot: draws a heatmap of the fold change of two masses (log2(intensity ratio))\n+\n+Output: \n+\n+- pdf with numbers and descriptive plots to check the quality of the mass-spectrometry imaging data\n+\n+Tip: \n+\n+- For additional heatmap images use the MSI ion images tool and to plot more mass spectra use the MSI massspectra tool. \n \n ]]>\n </help>\n' |
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| diff -r b86a66dd1a16 -r 52ef77866de8 test-data/inputcalibrantfile2.txt --- 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 |
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| @@ -1,3 +1,3 @@ 869.51 mass1 -1001.62 mass2 -1023.6 mass3 +1111.1 mass2 +1296.7 mass3 |
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| diff -r b86a66dd1a16 -r 52ef77866de8 test-data/inputpeptides.csv --- a/test-data/inputpeptides.csv Tue May 08 02:36:43 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -152 mass1 -328.9 mass2 -185.2 mass3 |
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| diff -r b86a66dd1a16 -r 52ef77866de8 test-data/inputpeptides.txt --- a/test-data/inputpeptides.txt Tue May 08 02:36:43 2018 -0400 +++ b/test-data/inputpeptides.txt Mon May 28 12:38:50 2018 -0400 |
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| @@ -1,3 +1,6 @@ +152 +328.9 +185.9 854.5 -1296.7 +1250.1 2000.8 |
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