diff preprocessing.xml @ 11:e86a8be551b9 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0c667acd7cc0d0ef6c4e979ca29372b8c0d92c23"

--- a/preprocessing.xml	Sun Sep 27 11:10:30 2020 +0000
+++ b/preprocessing.xml	Tue Oct 06 08:12:49 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.0">
+<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1">
     <description>
         mass spectrometry imaging preprocessing
     </description>
@@ -336,10 +336,12 @@
 
                 #if str($processed_cond.processed_file) == "processed":
 
-                msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
+                msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
                 
                 #else 
-                    msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
+                    ## continuous file cannot be binned from m/z to m/z, therefore first cut m/z range and then do mzbin:
+                    msidata = msidata[mz(msidata) >= $method.methods_conditional.mz_range.min_mz & mz(msidata) <= $method.methods_conditional.mz_range.max_mz,]
+                    msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
                 #end if