--- a/combine.xml	Thu Feb 28 09:28:34 2019 -0500
+++ b/combine.xml	Fri Mar 22 08:18:29 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.2">
+<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.3">
     <description>
         combine several mass spectrometry imaging datasets into one
     </description>
@@ -155,6 +155,7 @@
         coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y]) ## shifts y coordinates according to tabular file
         pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel
         msidata_$i\$combined_sample = rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))
+        ## store number of file
         pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
         #silent $pixelcoords.append('pixelcoords_'+str($i))
         colnames(pixelcoords_$i)[3] = "file_number"
@@ -253,6 +254,7 @@
     msidata_combined = do.call(combine, datasetlist)
 
     msidata = msidata_combined
+
     ## save msidata as imzML file
     #if str($imzml_output) == "imzml_format":
         writeImzML(msidata, "out")
@@ -410,13 +412,13 @@
     </configfiles>
     <inputs>
         <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
-            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="centroids" type="boolean" label="Is the input data centroided (picked)" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
+            label="MSI data"
+            help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/>
+        <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
         <conditional name="processed_cond">
-            <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
-                <option value="no_processed" selected="True">not a processed imzML</option>
-                <option value="processed">processed imzML</option>
+            <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
+                <option value="no_processed" selected="True">no</option>
+                <option value="processed">yes</option>
             </param>
             <when value="no_processed"/>
             <when value="processed">
@@ -457,8 +459,8 @@
         </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>
     <outputs>