| Previous changeset 6:5a5b5a8fa8a0 (2018-06-19) Next changeset 8:6cd561bbb7ee (2018-08-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_ion_images commit 8087490eb4dcaf4ead0f03eae4126780d21e5503 |
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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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| diff -r 5a5b5a8fa8a0 -r db0cf8eb4395 msi_ion_images.xml --- a/msi_ion_images.xml Tue Jun 19 18:07:40 2018 -0400 +++ b/msi_ion_images.xml Fri Jul 06 14:13:35 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.2"> +<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.3"> <description> mass spectrometry imaging m/z heatmaps </description> @@ -34,10 +34,15 @@ ## Read MALDI Imaging dataset + #if $infile.ext == 'imzml' - msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") + #if str($processed_cond.processed_file) == "processed": + msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") + #else + msidata <- readImzML('infile', attach.only=TRUE) + #end if #elif $infile.ext == 'analyze75' - msidata = readAnalyze('infile') + msidata = readAnalyze('infile', attach.only=TRUE) #else load('infile.RData') #end if @@ -59,17 +64,17 @@ 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) +minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2) +maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2) +medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2) ## Number of intensities > 0 -npeaks= sum(spectra(msidata)[]>0) +npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE) ## Spectra multiplied with m/z (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)[]) +TICs = colSums(spectra(msidata)[], na.rm=TRUE) NumemptyTIC = sum(TICs == 0) ## Processing informations @@ -219,11 +224,20 @@ <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="accuracy" type="float" value="50" label="Only for processed imzML files: enter mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> - <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> - <option value="mz" >mz</option> - <option value="ppm" selected="True" >ppm</option> - </param> + <conditional name="processed_cond"> + <param name="processed_file" type="select" label="Is the input file a processed imzML file "> + <option value="no_processed" selected="True">not a processed imzML</option> + <option value="processed">processed imzML</option> + </param> + <when value="no_processed"/> + <when value="processed"> + <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> + <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> + <option value="mz" >mz</option> + <option value="ppm" selected="True" >ppm</option> + </param> + </when> + </conditional> <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/> <param name="massfile" type="data" format="tabular" label="Tabular file with m/z and names" help="first column m/z, second column m/z name, tab separated file"/> @@ -239,7 +253,7 @@ </param> <param name="plusminus_dalton" value="0.25" type="float" label="M/z range" help="plusminus m/z window in Dalton"/> <param name="strip" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/> - <param name="colorkey" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/> + <param name="colorkey" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/> <conditional name="image_cond"> <param name="image_type" type="select" label="Select the image type"> <option value="standard_image" selected="True">standard</option> |
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