| Previous changeset 3:616b98c235fb (2018-04-23) Next changeset 5:2b9fa240e261 (2018-06-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_ion_images commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 |
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modified:
msi_ion_images.xml test-data/Analyze75.hdr test-data/Analyze75.img test-data/Analyze75.t2m test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_rdata.pdf test-data/inputpeptides2.tabular test-data/tabular_LM8file16.tabular test-data/tabular_analyze75.tabular test-data/tabular_imzml.tabular test-data/tabular_rdata.tabular |
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added:
test-data/empty_spectra.rdata test-data/preprocessed.rdata |
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removed:
test-data/LM8_file16.rdata test-data/preprocessing_results1.RData |
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| diff -r 616b98c235fb -r 9746576123c9 msi_ion_images.xml --- a/msi_ion_images.xml Mon Apr 23 17:18:53 2018 -0400 +++ b/msi_ion_images.xml Mon May 28 12:37:17 2018 -0400 |
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| b'@@ -1,22 +1,21 @@\n-<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.7.0.3">\n+<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.0">\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="1.10.0">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 \'${infile.extra_files_path}/ibd\' infile.ibd &&\n+ ln -s \'${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@@ -26,25 +25,25 @@\n </command>\n <configfiles>\n <configfile name="MSI_heatmaps"><![CDATA[\n-################################# load libraries and read file #########################\n+\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+ msidata = readImzML(\'infile\')\n #elif $infile.ext == \'analyze75\'\n- msidata = readMSIData(\'infile.hdr\')\n+ msidata = readAnalyze(\'infile\')\n #else\n load(\'infile.RData\')\n #end if\n \n \n-###################################### file properties in numbers ######################\n+###################################### file properties in numbers ##############\n \n ## Number of features (mz)\n maxfeatures = length(features(msidata))\n@@ -81,58 +80,64 @@\n \n ## normalization\n if (length(processinginfo@normalization) == 0) {\n- normalizationinfo=\'FALSE\'\n+ normalizationinfo=\'FALSE\'\n } else {\n- normalizationinfo=processinginfo@normalization\n+ normalizationinfo=processinginfo@normalization\n }\n ## smoothing\n if (length(processinginfo@smoothing) == 0) {\n- smoothinginfo=\'FALSE\'\n+ smoothinginfo=\'FALSE\'\n } else {\n- smoothinginfo=processinginfo@smoothing\n+ smoothinginfo=processinginfo@smoothing\n }\n ## baseline\n if (length(processinginfo@baselineReduction) == 0) {\n- baselinereductioninfo=\'FALSE\'\n+ baselinereductioninfo=\'FALSE\'\n } else {\n- baselinereductioninfo=processinginfo@baselineReduction\n+ baselinereductioninfo=processinginfo@baselineReduction\n }\n ## peak picking\n if (length(processinginfo@peakPicking) == 0) {\n- peakpickinginfo=\'FALSE\'\n+ peakpickinginfo=\'FALSE\'\n } else {\n- peakpickinginfo=processinginfo@peakPicking\n+ peakpickinginfo=processinginfo@peakPicking\n }\n \n-\n-### Read tabular file with peptide masses for heatmap images: \n+##################################### read and filter input masses ##############\n \n input_list = read.delim("$massfile", header = FALSE, stringsAsFactors = FALSE)\n- if (ncol(input_list) == 1)\n- {\n- input_list = cbind(input_list, input_list)\n- }\n+\n+### in case input file had only one column with mz values but not names, duplicate mz values and use as names:\n \n- ### calculate how many input masses are valid: \n- inputmasses = input_l'..b'9,17 @@\n <output name="pixel_count" file="tabular_analyze75.tabular"/>\n </test>\n <test>\n- <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>\n+ <param name="infile" value="preprocessed.rdata" ftype="rdata"/>\n <param name="massfile" value="inputpeptides.tabular" ftype="tabular"/>\n- <param name="plusminus_dalton" value="0.1"/>\n+ <param name="plusminus_dalton" value="0.5"/>\n <param name="filename" value="Testfile_rdata"/>\n <output name="plots" file="Heatmaps_rdata.pdf" compare="sim_size" delta="20000"/>\n <output name="pixel_count" file="tabular_rdata.tabular"/>\n </test>\n <test>\n- <param name="infile" value="LM8_file16.rdata" ftype="rdata"/>\n+ <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>\n <param name="massfile" value="inputpeptides2.tabular" ftype="tabular"/>\n- <param name="plusminus_dalton" value="0.1"/>\n+ <param name="plusminus_dalton" value="0.5"/>\n <param name="filename" value="Testfile_rdata"/>\n <output name="plots" file="Heatmaps_LM8_file16.pdf" compare="sim_size" delta="20000"/>\n <output name="pixel_count" file="tabular_LM8file16.tabular"/>\n@@ -280,26 +277,35 @@\n </tests>\n <help><![CDATA[\n \n-Heatmaps for different masses in mass-spectrometry imaging data as pdf output. \n \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 the Cardinal image function to plot the intensity distribution of interesting masses of mass-spectrometry imaging data. \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+- 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-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+Tabular file with masses:\n+\n+- tab separated file (.tabular), datatype in Galaxy must be tabular otherwise file will not appear in selection window (if Galaxy auto-detection was wrong, datatype can be changed by pressing button with the pen (edit attributes))\n - first column must contain masses (separate point numbers by point, not comma)\n - optionally a second column with names for the masses can be provided\n-- no empty fields or letters are allowed (tool crashes with empty fields and a single letter prohibits generation of images)\n+- no empty fields or letters are allowed in the first column\n+\n+Output:\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+- Pdf with the heatmap images\n+- Tabular with masses that were in the mass range and their occurence over all pixels (absolute and in %)\n \n+Troubleshooting:\n+\n+- no heatmaps are plotted when tabular file doesn\'t fulfill the criteria described above\n+- no heatmaps are plotted when the input mass spectrometry imaging file has no intensities > 0\n+- out of thetabular file only masses with > 1.5-2% pixel coverage can be used with the contrast enhance and image smoothing functions, as both crash when a mass has not enough intensity values\n \n ]]>\n </help>\n' |
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| diff -r 616b98c235fb -r 9746576123c9 test-data/inputpeptides2.tabular --- a/test-data/inputpeptides2.tabular Mon Apr 23 17:18:53 2018 -0400 +++ b/test-data/inputpeptides2.tabular Mon May 28 12:37:17 2018 -0400 |
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| @@ -1,1 +1,4 @@ 854.5 +1111.1 +1296.7 +1305.1 |
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| diff -r 616b98c235fb -r 9746576123c9 test-data/tabular_LM8file16.tabular --- a/test-data/tabular_LM8file16.tabular Mon Apr 23 17:18:53 2018 -0400 +++ b/test-data/tabular_LM8file16.tabular Mon May 28 12:37:17 2018 -0400 |
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| @@ -1,2 +1,2 @@ - inputmz countpixels percentpixels -1 854.5 0 0 +inputmz countpixels percentpixels +1111.1 0 0 |
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| diff -r 616b98c235fb -r 9746576123c9 test-data/tabular_analyze75.tabular --- a/test-data/tabular_analyze75.tabular Mon Apr 23 17:18:53 2018 -0400 +++ b/test-data/tabular_analyze75.tabular Mon May 28 12:37:17 2018 -0400 |
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| @@ -1,2 +1,3 @@ - inputmz countpixels percentpixels -1 854.5 2 22.2 +inputmz countpixels percentpixels +1296.7 9 100 +1305.1 9 100 |
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| diff -r 616b98c235fb -r 9746576123c9 test-data/tabular_imzml.tabular --- a/test-data/tabular_imzml.tabular Mon Apr 23 17:18:53 2018 -0400 +++ b/test-data/tabular_imzml.tabular Mon May 28 12:37:17 2018 -0400 |
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| @@ -1,4 +1,4 @@ - inputmz countpixels percentpixels -1 152 9 100 -2 328.9 9 100 -3 185.2 6 66.7 +inputmz countpixels percentpixels +152 9 100 +328.9 9 100 +185.2 6 66.7 |
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| diff -r 616b98c235fb -r 9746576123c9 test-data/tabular_rdata.tabular --- a/test-data/tabular_rdata.tabular Mon Apr 23 17:18:53 2018 -0400 +++ b/test-data/tabular_rdata.tabular Mon May 28 12:37:17 2018 -0400 |
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| @@ -1,4 +1,2 @@ - inputmz countpixels percentpixels -1 152 9 100 -2 328.9 9 100 -3 185.2 6 66.7 +inputmz countpixels percentpixels +328.9 9 100 |