diff DecoyDatabase.xml @ 1:bf3b4e5c0dcb draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

--- a/DecoyDatabase.xml	Wed Mar 01 12:16:29 2017 -0500
+++ b/DecoyDatabase.xml	Tue Apr 18 16:01:49 2017 -0400
@@ -23,13 +23,28 @@
   -decoy_string     "$param_decoy_string"
 #end if
 #if $param_decoy_string_position:
-  -decoy_string_position $param_decoy_string_position
+  -decoy_string_position
+  #if " " in str($param_decoy_string_position):
+    "$param_decoy_string_position"
+  #else
+    $param_decoy_string_position
+  #end if
 #end if
 #if $param_append:
-  -append $param_append
+  -append
+  #if " " in str($param_append):
+    "$param_append"
+  #else
+    $param_append
+  #end if
 #end if
 #if $param_method:
-  -method $param_method
+  -method
+  #if " " in str($param_method):
+    "$param_method"
+  #else
+    $param_method
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
@@ -73,14 +88,12 @@
   <outputs>
     <data name="param_out" format="fasta"/>
   </outputs>
-
-   <tests>
-        <test>
-            <param name="param_in" value="DecoyDatabase_input.fasta"/>
-            <output name="param_out" file="DecoyDatabase_output.fasta"/>
-        </test>
-    </tests>
-
+  <tests>
+    <test>
+        <param name="param_in" value="DecoyDatabase_input.fasta"/>
+        <output name="param_out" file="DecoyDatabase_output.fasta"/>
+    </test>
+  </tests>
   <help>Create decoy peptide databases from normal ones.