--- a/filtering.xml	Thu Feb 28 09:22:46 2019 -0500
+++ b/filtering.xml	Fri Mar 22 08:14:21 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.2">
+<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.3">
     <description>tool for filtering mass spectrometry imaging data</description>
     <macros>
         <import>macros.xml</import>
@@ -58,6 +58,9 @@
         ## Store features for QC plot
         featuresinfile = mz(msidata)
 
+        all_df = cbind(coord(msidata)[,1:2], rep("removed pixels", times=ncol(msidata)))
+        colnames(all_df)[3] = "annotation"
+
 ## Next steps will only run if there are more than 0 pixels/features in the file
 
 if (ncol(msidata)>0 & nrow(msidata) >0)
@@ -138,8 +141,11 @@
     ############################# QC data #####################################
 
     ## dataframe for QC of pixel distribution
-    position_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata)))
-    colnames(position_df)[3] = "annotation"
+
+    remaining_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata)))
+    colnames(remaining_df)[3] = "annotation"
+    position_df = rbind(all_df, remaining_df) 
+    position_df[row.names(unique(position_df[,c("x", "y")])),]
     position_df\$annotation = factor(position_df\$annotation)
     gc()
 
@@ -444,8 +450,8 @@
         </conditional>
         <param name="imzml_output" type="select" display = "radio" optional = "False"
                label="Output format" help= "Choose the output format">
-                <option value="imzml_format" selected="True">imzML</option>
-                <option value="rdata_format">RData</option>
+                <option value="imzml_format" >imzML</option>
+                <option value="rdata_format" selected="True" >RData</option>
         </param>
     </inputs>
 
@@ -593,7 +599,7 @@
 **Output**
 
 - MSI data as imzML file or .RData (can be read with the Cardinal package in R)
-- pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z
+- pdf with heatmap showing the pixels that are removed and kept as well as histograms of kept and removed m/z
 
 
         ]]>