Mercurial > repos > galaxyp > msi_ion_images
changeset 6:5a5b5a8fa8a0 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_ion_images commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
| author | galaxyp |
|---|---|
| date | Tue, 19 Jun 2018 18:07:40 -0400 |
| parents | 2b9fa240e261 |
| children | db0cf8eb4395 |
| files | 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 |
| diffstat | 5 files changed, 10 insertions(+), 5 deletions(-) [+] |
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--- a/msi_ion_images.xml Mon Jun 11 17:33:52 2018 -0400 +++ b/msi_ion_images.xml Tue Jun 19 18:07:40 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.1"> +<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.2"> <description> mass spectrometry imaging m/z heatmaps </description> @@ -35,7 +35,7 @@ ## Read MALDI Imaging dataset #if $infile.ext == 'imzml' - msidata = readImzML('infile') + msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") #elif $infile.ext == 'analyze75' msidata = readAnalyze('infile') #else @@ -130,7 +130,7 @@ ############################# I) numbers #################################### properties = c("Number of m/z features", - "Range of m/z values [Da]", + "Range of m/z values", "Number of pixels", "Range of x coordinates", "Range of y coordinates", @@ -181,7 +181,7 @@ print("standard image") print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", - smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey, + smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy), main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} @@ -194,7 +194,7 @@ print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", - colorkey=$colorkey, + colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy), main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} #elif str($strip) =="FALSE": @@ -219,6 +219,11 @@ <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> <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"/>