diff tools/clinod/clinod.xml @ 5:9485cdfca57e draft

v0.0.8 internal changes

--- a/tools/clinod/clinod.xml	Thu Nov 20 06:15:49 2014 -0500
+++ b/tools/clinod/clinod.xml	Wed Aug 05 10:58:54 2015 -0400
@@ -1,20 +1,20 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.7">
+<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.8">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
     <requirements>
         <requirement type="binary">java</requirement>
         <requirement type="package" version="1.3">clinod</requirement>
     </requirements>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <command>
 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder
 ##containing both clinod-1.3.jar and the batchman binary:
 java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence
 ##TODO - Make the -clean_sequence argument a parameter?
     </command>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <inputs>
         <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
     </inputs>