--- a/Get_ms-ms_observations.xml	Fri Feb 01 11:48:49 2019 -0500
+++ b/Get_ms-ms_observations.xml	Wed Mar 13 09:34:37 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.01.1">
+<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.26">
     <description>[Peptide Atlas]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -16,7 +16,7 @@
             --column_number="$input.ncol"
             --header="$input.header"
         #end if
-        --atlas=${",".join([$__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])}
+        --atlas=${",".join([str(ref) if "peptide_atlas" in str(ref).split("/") else $__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])}
         --output="$output"
     </command>
 
@@ -41,7 +41,9 @@
             <when value="file" >
                 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
                 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
-                <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
+                <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
+                    <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+                </param>
             </when>
         </conditional>
         <!-- Peptide Atlas options -->