diff SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml @ 4:10627af23f10 draft

planemo upload

--- a/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml	Fri Jul 10 10:38:43 2015 -0400
+++ b/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml	Tue Dec 15 05:18:02 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="sniplay_density" name="SNP density" version="1.2.0">
+<tool id="sniplay_density" name="SNP density" version="1.3.0">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description> Calculate SNP densities along chromosome from HapMap</description>
@@ -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>
 <!--
@@ -19,7 +25,7 @@
     <command interpreter="bash">
 	calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step
     </command>
-   
+
     <!-- [REQUIRED] Input files and tool parameters -->
     <inputs>
 	<param name="filein" type="data" format="txt" optional="false" label="Hapmap input" />
@@ -32,22 +38,14 @@
 	<data name="fileout" type="data" format="tabular" label="${fileout_label}" />
 	<data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" />
     </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="input" value="input_test.txt" />
-         <output name="output" file="output_test.txt" />
+        <test> 
+         <param name="filein" value="SNPden-hapmap" />
+         <param name="step" value="200000" />
+         <output name="fileout" file="SNPden-result.txt" />
+         <output name="fileout_bysample" file="SNPden-result_bysample.txt" />
         </test>
--->
         <!-- [HELP] Multiple tests can be defined with different parameters -->
 <!--
         <test>