--- a/add_expression_data.xml	Thu Jun 27 03:56:26 2019 -0400
+++ b/add_expression_data.xml	Wed Jan 22 14:59:04 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="rna_abbased_data" name="Add expression data" version="2019.06.27">
+<tool id="rna_abbased_data" name="Add expression data" version="2020.01.22">
 <description> (RNAseq or Immuno-assays)[Human Protein Atlas]
 </description>
 <requirements>
@@ -9,16 +9,24 @@
 </stdio>
 <command><![CDATA[
 
-  #if $inputtype.filetype == "copy_paste": 
-  
-    Rscript $__tool_directory__/add_expression_HPA.R --inputtype="copypaste" --input='$inputtype.genelist' --atlas="$__tool_directory__/proteinatlas.csv" --select='$options.hpaparams' --output='$output'  
+    Rscript $__tool_directory__/add_expression_HPA.R
+    --input='$inputtype.genelist'
+    --select='$options.hpaparams'
+    --output='$output' 
+    
+    #if $inputtype.filetype == "copy_paste": 
+        --inputtype="copypaste"    
+    #else 
+        --inputtype="tabfile" 
+        --header='$inputtype.header' 
+        --column='$inputtype.column'  
+    #end if
 
-  #else 
-  
-    Rscript $__tool_directory__/add_expression_HPA.R --inputtype="tabfile" --input='$inputtype.genelist' --header='$inputtype.header' --atlas="$__tool_directory__/proteinatlas.csv" --column='$inputtype.column' --select='$options.hpaparams' --output='$output'  
-
-  #end if
-   
+    #if "protein_atlas" in str($input.ref_file).split("/")
+    --hpa_ref="$input.ref_file"
+    #else 
+    --hpa_ref="$__tool_directory__/$input.ref_file"
+    #end if
 
 ]]></command>