| Previous changeset 0:385e8a4accd9 (2017-11-27) Next changeset 2:b2ad54eabcca (2018-03-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a |
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modified:
msi_ion_images.xml test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_rdata.pdf |
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added:
test-data/inputpeptides.tabular test-data/inputpeptides2.tabular |
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removed:
test-data/inputpeptides.csv test-data/inputpeptides.txt |
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| diff -r 385e8a4accd9 -r 845fee459824 msi_ion_images.xml --- a/msi_ion_images.xml Mon Nov 27 13:49:35 2017 -0500 +++ b/msi_ion_images.xml Thu Mar 01 08:25:18 2018 -0500 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.7.0">\n+<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.7.0.1">\n <description>\n mass spectrometry imaging heatmaps\n </description>\n@@ -36,24 +36,13 @@\n ## Read MALDI Imaging dataset\n \n #if $infile.ext == \'imzml\'\n- msidata <- readMSIData(\'infile.imzML\')\n+ msidata = readMSIData(\'infile.imzML\')\n #elif $infile.ext == \'analyze75\'\n- msidata <- readMSIData(\'infile.hdr\')\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@@ -115,12 +104,32 @@\n peakpickinginfo=processinginfo@peakPicking\n }\n \n-### calculate how many input masses are valid: \n-inputmasses = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]\n+#if $massfile:\n+ ### Read tabular file with peptide masses for plots and heatmap images: \n+ input_list = read.delim("$massfile", header = FALSE, stringsAsFactors = FALSE)\n+ if (ncol(input_list) == 1)\n+ {\n+ input_list = cbind(input_list, input_list)\n+ }\n+ ### calculate how many input masses are valid: \n+ inputmasses = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]\n \n-inputmz = inputmasses[,1]\n-inputnames = inputmasses[,2]\n+ inputmz = inputmasses[,1]\n+ inputnames = inputmasses[,2]\n+#else\n+ input_list = data.frame(0, 0)\n+ inputmz = 0\n+#end if\n+\n \n+countpixels = rowSums(spectra(msidata)[features(msidata, mz=inputmz),]>0)\n+percentpixels = round(countpixels/pixelcount*100, digits=1)\n+valuesdataframe = cbind(inputmz, cbind(countpixels, percentpixels))\n+\n+\n+write.table(valuesdataframe, file="$pixel_count", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\\t")\n+\n+colnames(input_list)[1:2] = c("mz", "name")\n properties = c("Number of mz features",\n "Range of mz values [Da]",\n "Number of pixels", \n@@ -136,7 +145,7 @@\n "Baseline reduction",\n "Peak picking",\n "Centroided", \n- paste0("# valid masses in ", "$filename"))\n+ paste0("# valid masses in ", "$massfile.display_name"))\n \n values = c(paste0(maxfeatures), \n paste0(minmz, " - ", maxmz), \n@@ -157,6 +166,9 @@\n \n property_df = data.frame(properties, values)\n \n+\n+\n+\n ######################################## PDF #############################################\n ##########################################################################################\n ##########################################################################################\n@@ -176,15 +188,19 @@\n \n if (npeaks > 0)\n {\n+\n if (length(inputmz) != 0)\n {\n+\n for (mass in 1:length(inputmz))\n {\n- print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),\n- lattice=TRUE, ylim = c(maximumy+1,minimumy-1), plusminus = $plusminusinDalton, contrast.enhance = "histogram", \n- main= paste0(mass, ") ", inputnames[mass], " (", round(inputmz[mass], digits = 2)," \xc2\xb1 ", $plusminusinDalton, " Da)")))\n+\n+\n+ print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),\n+ lattice=TRUE, ylim = c(maximumy+1,minimumy-1), plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", \n+ main= paste0(mass, ") ", inputnames'..b'intensity"/>\n </outputs>\n <tests>\n <test>\n@@ -211,9 +238,10 @@\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="massfile" value="inputpeptides.tabular" ftype="tabular"/>\n+ <param name="plusminus_dalton" value="0.25"/>\n <param name="filename" value="Testfile_imzml"/>\n+ <param name="image_contrast" value="histogram"/>\n <output name="plots" file="Heatmaps_imzml.pdf" compare="sim_size" delta="20000"/>\n </test>\n \n@@ -223,37 +251,48 @@\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="massfile" value="inputpeptides2.tabular" ftype="tabular"/>\n+ <param name="plusminus_dalton" value="0.5"/>\n <param name="filename" value="Testfile_analyze75"/>\n+ <param name="image_smoothing" value="gaussian"/>\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="massfile" value="inputpeptides.tabular" ftype="tabular"/>\n+ <param name="plusminus_dalton" 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="massfile" value="inputpeptides2.tabular" ftype="tabular"/>\n+ <param name="plusminus_dalton" 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+Heatmaps for different masses in mass-spectrometry imaging data as pdf output. \n \n-Input data: 3 types of input data can be used:\n+Input data: \n+\n+3 types of mass-spectrometry imaging 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+tabular file with masses: \n+- tab separated file (.tabular), datatype in Galaxy must be tabular (if Galaxy auto-detection was wrong, datatype can be changed by pressing the pen button)\n+- no empty fields or letters are allowed (tool crashes with empty fields and a single letter prohibits generation of images)\n+- separate point numbers by point (a single number with comma prohibits generation of images)\n+\n+Trouble shooting: \n+- no heatmaps are plotted when tabular file contains letters or point numbers with commas or when the input MSI file had no intensities > 0\n+- contrast enhance functions need masses with intensities > 0 in about 1.5% of all pixels - tool crashes when contrast enhance is used on too few intensities\n+\n \n ]]>\n </help>\n' |
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| diff -r 385e8a4accd9 -r 845fee459824 test-data/Heatmaps_LM8_file16.pdf |
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| diff -r 385e8a4accd9 -r 845fee459824 test-data/Heatmaps_imzml.pdf |
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| diff -r 385e8a4accd9 -r 845fee459824 test-data/Heatmaps_rdata.pdf |
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| diff -r 385e8a4accd9 -r 845fee459824 test-data/inputpeptides.csv --- a/test-data/inputpeptides.csv Mon Nov 27 13:49:35 2017 -0500 +++ /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 385e8a4accd9 -r 845fee459824 test-data/inputpeptides.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides.tabular Thu Mar 01 08:25:18 2018 -0500 |
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| @@ -0,0 +1,3 @@ +152 mass1 +328.9 mass2 +185.2 mass3 |
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| diff -r 385e8a4accd9 -r 845fee459824 test-data/inputpeptides.txt --- a/test-data/inputpeptides.txt Mon Nov 27 13:49:35 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -854.5 -1296.7 -2000.8 |
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| diff -r 385e8a4accd9 -r 845fee459824 test-data/inputpeptides2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides2.tabular Thu Mar 01 08:25:18 2018 -0500 |
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| @@ -0,0 +1,3 @@ +854.5 +1296.7 +2000.8 |