# HG changeset patch
# User galaxyp
# Date 1529446024 14400
# Node ID d05bd881af3d43a8f93b346145631773bfe61c53
# Parent  91bba24867733bbc4166ddb04ee5da1b509fb35c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5

diff -r 91bba2486773 -r d05bd881af3d msi_combine.xml
--- a/msi_combine.xml	Mon Jun 11 17:33:28 2018 -0400
+++ b/msi_combine.xml	Tue Jun 19 18:07:04 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.1">
+<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.2">
     <description>
         combine several mass spectrometry imaging datasets into one
     </description>
@@ -68,7 +68,7 @@
 #for $i, $infile in enumerate($infiles):
 
     #if $infile.ext == 'imzml'
-        msidata_$i <- readImzML('infile_${i}')
+        msidata_$i <- readImzML('infile_${i}', mass.accuracy=$accuracy, units.accuracy = "$units")
     #elif $infile.ext == 'analyze75'
         msidata_$i <- readAnalyze('infile_${i}')
     #else
@@ -209,7 +209,8 @@
            theme_bw()+
            theme(text=element_text(family="ArialMT", face="bold", size=15))+
            theme(legend.position="bottom",legend.direction="vertical")+
-           guides(fill=guide_legend(ncol=4,byrow=TRUE))
+           theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+
+           guides(fill=guide_legend(ncol=5,byrow=TRUE))
     coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
     coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
     for(file_count in 1:nrow(coord_labels))
@@ -239,8 +240,13 @@
     </configfiles>
     <inputs>
         <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
-            label="MSI rawdata as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
+            label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
             help="load imzml and ibd file by uploading composite datatype imzml"/>
+        <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="combine_conditional">
             <param name="combine_method" type="select" label="Select the way you want to combine multiple files" help="More detailed help can be found in the help section at the bottom">
                 <option value="automatic_combine" selected="True" >automatic combination</option>
diff -r 91bba2486773 -r d05bd881af3d test-data/112_auto_combined_QC.pdf
Binary file test-data/112_auto_combined_QC.pdf has changed
diff -r 91bba2486773 -r d05bd881af3d test-data/123_combined_QC.pdf
Binary file test-data/123_combined_QC.pdf has changed
diff -r 91bba2486773 -r d05bd881af3d test-data/123_no_combi_QC.pdf
Binary file test-data/123_no_combi_QC.pdf has changed
diff -r 91bba2486773 -r d05bd881af3d test-data/12_combined_QC.pdf
Binary file test-data/12_combined_QC.pdf has changed