diff ped2bed/ped2bed.xml @ 4:10627af23f10 draft

planemo upload

--- a/ped2bed/ped2bed.xml	Fri Jul 10 10:38:43 2015 -0400
+++ b/ped2bed/ped2bed.xml	Tue Dec 15 05:18:02 2015 -0500
@@ -3,7 +3,12 @@
 	<requirements>
 		<requirement type="package" version="1.07">plink</requirement>
 	</requirements>
-	<command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs
+    <!-- [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>
+    <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs
     </command>
 	<inputs>
 		<param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/>
@@ -15,20 +20,18 @@
 		<data format="txt" name="bim" label="Bim file"/>
 		<data format="txt" name="logs" label="All Logs"/>
 	</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 -->
         <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
         <test>
+         <param name="ped" value="ped2bed-input.ped" />
+	 <param name="map" value="ped2bed-input.map" />
+         <output name="bed" file="ped2bed-result.bed" />
+         <output name="fam" file="ped2bed-result.fam" />
+         <output name="bim" file="ped2bed-result.bim" />
         </test>
--->
     </tests>
 	<help>