--- a/VCF2Hapmap/vcf2FastaAndHapmap.xml	Fri Jul 10 10:38:43 2015 -0400
+++ b/VCF2Hapmap/vcf2FastaAndHapmap.xml	Tue Dec 15 05:18:02 2015 -0500
@@ -8,6 +8,12 @@
         <requirement type="binary">perl</requirement>
     </requirements>
     
+    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
+    <stdio>
+        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+
     <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
     <version_command>
 <!--
@@ -17,7 +23,7 @@
     
     <!-- [REQUIRED] The command to execute -->
     <command interpreter="bash">
-	vcf2FastaAndHapmap.sh $filein $fileout_label $fileout $optional.file_opt 
+	vcf2FastaAndHapmap.sh $filein $fileout $optional.file_opt 
 	#if str( $optional.file_opt ) != "none":
 		$fileout_seq $fileout_fa1 $filefasta 
 		#if str( $optional.file_opt ) == "fasta_gff":
@@ -58,27 +64,29 @@
 	</data>
     </outputs>
     
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
     <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
     <tests>
         <!-- [HELP] Test files have to be in the ~/test-data directory -->
         <test>
-         <param name="filein" value="sample.vcf" />
-         <param name="otpional.file_opt" value="none" />
-         <output name="fileout" file="result1.hapmap" />
+         <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
+         <param name="file_opt" value="none" />
+         <output name="fileout" file="vcf2fastaAndHapmap-result1.hapmap" />
         </test>
 	<test>
-         <param name="filein" value="sample.vcf" />
-	 <param name="otpional.file_opt" value="fasta" />
-         <param name="filefasta" value="reference.fa" />
-         <output name="fileout" file="result2.hapmap" />
-         <output name="fileout_seq" file="result2.flanking.txt" />
-         <output name="fileout_fa1" file="result2.gene_alignment.fas" />
+         <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
+	 <param name="file_opt" value="fasta" />
+         <param name="filefasta" value="vcf2fastaAndHapmap-reference.fa" />
+         <output name="fileout" file="vcf2fastaAndHapmap-result2.hapmap" />
+         <output name="fileout_seq" file="vcf2fastaAndHapmap-result2.flanking.txt" />
+        </test>
+	<test>
+         <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
+	 <param name="file_opt" value="fasta_gff" />
+         <param name="filefasta" value="vcf2fastaAndHapmap-reference.fa" />
+         <param name="filegff" value="vcf2fastaAndHapmap-reference.gff" />
+         <output name="fileout" file="vcf2fastaAndHapmap-result3.hapmap" />
+         <output name="fileout_seq" file="vcf2fastaAndHapmap-result3.flanking.txt" />
+         <output name="fileout_fa1" file="vcf2fastaAndHapmap-result3.gene_alignment.fas" />
         </test>
     </tests>