# HG changeset patch
# User galaxyp
# Date 1529445912 14400
# Node ID 1a7cc5e144302ec5a845e2238f9221db3b57efb5
# Parent  a851b4e8fba7459e655517c0a6d387878622b67a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_ion_images commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5

diff -r a851b4e8fba7 -r 1a7cc5e14430 msi_ion_images.xml
--- a/msi_ion_images.xml	Mon Jun 11 17:31:51 2018 -0400
+++ b/msi_ion_images.xml	Tue Jun 19 18:05:12 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"/>
diff -r a851b4e8fba7 -r 1a7cc5e14430 test-data/Heatmaps_LM8_file16.pdf
Binary file test-data/Heatmaps_LM8_file16.pdf has changed
diff -r a851b4e8fba7 -r 1a7cc5e14430 test-data/Heatmaps_analyze75.pdf
Binary file test-data/Heatmaps_analyze75.pdf has changed
diff -r a851b4e8fba7 -r 1a7cc5e14430 test-data/Heatmaps_imzml.pdf
Binary file test-data/Heatmaps_imzml.pdf has changed
diff -r a851b4e8fba7 -r 1a7cc5e14430 test-data/Heatmaps_rdata.pdf
Binary file test-data/Heatmaps_rdata.pdf has changed