diff VCFToolsStats/vcfToolsStats.xml @ 3:612066e3f57d draft

Uploaded

--- a/VCFToolsStats/vcfToolsStats.xml	Fri Jul 10 04:16:17 2015 -0400
+++ b/VCFToolsStats/vcfToolsStats.xml	Mon Nov 09 05:18:45 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="sniplay_vcftoolsstats" name="VCFtools Stats" version="1.0.0">
+<tool id="sniplay_vcftoolsstats" name="VCFtools Stats" version="1.1.0">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description> </description>
@@ -9,16 +9,15 @@
 	<requirement type="package" version="0.1.12b">vcftools</requirement>
     </requirements>
     
-    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
-    <version_command>
-<!--
-        tool_binary -v
--->
-    </version_command>
+    <!-- [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>
     
     <!-- [REQUIRED] The command to execute -->
     <command interpreter="perl">
-	vcfToolsStats.sh $filein $fileout_label $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog
+	vcfToolsStats.sh $filein $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog
     </command>
      
     <!-- [REQUIRED] Input files and tool parameters -->
@@ -36,12 +35,6 @@
 	<data name="filelog" format="txt" label="${fileout_label}.log" />
     </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 -->
@@ -51,7 +44,6 @@
          <output name="fileout_het" file="result.het" />
          <output name="fileout_imiss" file="result.imiss" />
          <output name="fileout_sum" file="result.TsTv.summary" />
-         <output name="filelog" file="result.log" />
         </test>
     </tests>