Mercurial > repos > galaxyp > msi_ion_images
comparison msi_ion_images.xml @ 7:db0cf8eb4395 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_ion_images commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
| author | galaxyp |
|---|---|
| date | Fri, 06 Jul 2018 14:13:35 -0400 |
| parents | 5a5b5a8fa8a0 |
| children | 6cd561bbb7ee |
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| 6:5a5b5a8fa8a0 | 7:db0cf8eb4395 |
|---|---|
| 1 <tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.2"> | 1 <tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.3"> |
| 2 <description> | 2 <description> |
| 3 mass spectrometry imaging m/z heatmaps | 3 mass spectrometry imaging m/z heatmaps |
| 4 </description> | 4 </description> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> | 6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> |
| 32 library(gridExtra) | 32 library(gridExtra) |
| 33 library(lattice) | 33 library(lattice) |
| 34 | 34 |
| 35 ## Read MALDI Imaging dataset | 35 ## Read MALDI Imaging dataset |
| 36 | 36 |
| 37 | |
| 37 #if $infile.ext == 'imzml' | 38 #if $infile.ext == 'imzml' |
| 38 msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") | 39 #if str($processed_cond.processed_file) == "processed": |
| 40 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") | |
| 41 #else | |
| 42 msidata <- readImzML('infile', attach.only=TRUE) | |
| 43 #end if | |
| 39 #elif $infile.ext == 'analyze75' | 44 #elif $infile.ext == 'analyze75' |
| 40 msidata = readAnalyze('infile') | 45 msidata = readAnalyze('infile', attach.only=TRUE) |
| 41 #else | 46 #else |
| 42 load('infile.RData') | 47 load('infile.RData') |
| 43 #end if | 48 #end if |
| 44 | 49 |
| 45 | 50 |
| 57 maximumx = max(coord(msidata)[,1]) | 62 maximumx = max(coord(msidata)[,1]) |
| 58 ## Range y coordinates | 63 ## Range y coordinates |
| 59 minimumy = min(coord(msidata)[,2]) | 64 minimumy = min(coord(msidata)[,2]) |
| 60 maximumy = max(coord(msidata)[,2]) | 65 maximumy = max(coord(msidata)[,2]) |
| 61 ## Range of intensities | 66 ## Range of intensities |
| 62 minint = round(min(spectra(msidata)[]), digits=2) | 67 minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2) |
| 63 maxint = round(max(spectra(msidata)[]), digits=2) | 68 maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2) |
| 64 medint = round(median(spectra(msidata)[]), digits=2) | 69 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2) |
| 65 ## Number of intensities > 0 | 70 ## Number of intensities > 0 |
| 66 npeaks= sum(spectra(msidata)[]>0) | 71 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE) |
| 67 ## Spectra multiplied with m/z (potential number of peaks) | 72 ## Spectra multiplied with m/z (potential number of peaks) |
| 68 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) | 73 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) |
| 69 ## Percentage of intensities > 0 | 74 ## Percentage of intensities > 0 |
| 70 percpeaks = round(npeaks/numpeaks*100, digits=2) | 75 percpeaks = round(npeaks/numpeaks*100, digits=2) |
| 71 ## Number of empty TICs | 76 ## Number of empty TICs |
| 72 TICs = colSums(spectra(msidata)[]) | 77 TICs = colSums(spectra(msidata)[], na.rm=TRUE) |
| 73 NumemptyTIC = sum(TICs == 0) | 78 NumemptyTIC = sum(TICs == 0) |
| 74 | 79 |
| 75 ## Processing informations | 80 ## Processing informations |
| 76 processinginfo = processingData(msidata) | 81 processinginfo = processingData(msidata) |
| 77 centroidedinfo = processinginfo@centroided # TRUE or FALSE | 82 centroidedinfo = processinginfo@centroided # TRUE or FALSE |
| 217 ]]></configfile> | 222 ]]></configfile> |
| 218 </configfiles> | 223 </configfiles> |
| 219 <inputs> | 224 <inputs> |
| 220 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" | 225 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" |
| 221 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> | 226 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> |
| 222 <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"/> | 227 <conditional name="processed_cond"> |
| 223 <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> | 228 <param name="processed_file" type="select" label="Is the input file a processed imzML file "> |
| 224 <option value="mz" >mz</option> | 229 <option value="no_processed" selected="True">not a processed imzML</option> |
| 225 <option value="ppm" selected="True" >ppm</option> | 230 <option value="processed">processed imzML</option> |
| 226 </param> | 231 </param> |
| 232 <when value="no_processed"/> | |
| 233 <when value="processed"> | |
| 234 <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"/> | |
| 235 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> | |
| 236 <option value="mz" >mz</option> | |
| 237 <option value="ppm" selected="True" >ppm</option> | |
| 238 </param> | |
| 239 </when> | |
| 240 </conditional> | |
| 227 <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/> | 241 <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/> |
| 228 <param name="massfile" type="data" format="tabular" label="Tabular file with m/z and names" | 242 <param name="massfile" type="data" format="tabular" label="Tabular file with m/z and names" |
| 229 help="first column m/z, second column m/z name, tab separated file"/> | 243 help="first column m/z, second column m/z name, tab separated file"/> |
| 230 <param name="image_contrast" type="select" label="Select a contrast enhancement function for the heatmap images" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots"> | 244 <param name="image_contrast" type="select" label="Select a contrast enhancement function for the heatmap images" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots"> |
| 231 <option value="none" selected="True">none</option> | 245 <option value="none" selected="True">none</option> |
| 237 <option value="gaussian">gaussian</option> | 251 <option value="gaussian">gaussian</option> |
| 238 <option value="adaptive">adaptive</option> | 252 <option value="adaptive">adaptive</option> |
| 239 </param> | 253 </param> |
| 240 <param name="plusminus_dalton" value="0.25" type="float" label="M/z range" help="plusminus m/z window in Dalton"/> | 254 <param name="plusminus_dalton" value="0.25" type="float" label="M/z range" help="plusminus m/z window in Dalton"/> |
| 241 <param name="strip" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/> | 255 <param name="strip" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/> |
| 242 <param name="colorkey" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/> | 256 <param name="colorkey" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/> |
| 243 <conditional name="image_cond"> | 257 <conditional name="image_cond"> |
| 244 <param name="image_type" type="select" label="Select the image type"> | 258 <param name="image_type" type="select" label="Select the image type"> |
| 245 <option value="standard_image" selected="True">standard</option> | 259 <option value="standard_image" selected="True">standard</option> |
| 246 <option value="lattice_image">lattice</option> | 260 <option value="lattice_image">lattice</option> |
| 247 </param> | 261 </param> |