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diff blat_wrapper.xml @ 1:c4ad58c4bc7d draft

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Add version_command element. Add test case from Joachim Jacob's blat wrapper: http://testtoolshed.g2.bx.psu.edu/view/joachim-jacob/blat . Add readme section to tool_dependencies.xml .
author crs4
date Mon, 28 Oct 2013 12:40:29 -0400
parents 0a71a7d35d09
children 6265acc179ff
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line diff
--- a/blat_wrapper.xml	Wed Oct 16 13:54:38 2013 -0400
+++ b/blat_wrapper.xml	Mon Oct 28 12:40:29 2013 -0400
@@ -3,6 +3,7 @@
   <requirements>
     <requirement type="package" version="35">blat</requirement>
   </requirements>
+  <version_command>blat|head -n 1</version_command>
   <command>
     blat $database $query -t=$databaseType.databaseType_select -q=$databaseType.queryType
     #if str($databaseType.tileSize)
@@ -195,8 +196,29 @@
       </change_format>
     </data>
   </outputs>
-
   <tests>
+    <test>
+      <param name="database" value="databasetest1.fasta" ftype="fasta" />
+      <param name="query" value="input83.fasta" ftype="fasta" />
+      <param name="databaseType_select" value="dna" />
+      <param name="queryType" value="dna" />
+      <param name="tileSize" value="11" />
+      <param name="minMatch" value="2" />
+      <param name="stepSize" value="11" />
+      <param name="oneOff" value="false" />
+      <param name="minScore" value="30" />
+      <param name="maxGap" value="2" />
+      <param name="mask_select" value="lower" />
+      <param name="qMask" value="lower" />
+      <param name="trimT" value="true" />
+      <param name="noTrimA" value="false" />
+      <param name="fine" value="false" />
+      <param name="maxIntron" value="750000" />
+      <param name="extendThroughN" value="false" />
+      <param name="out" value="blast8" />
+      <output name="logfile" file="log.txt" />
+      <output name="output" file="outputtest1.txt" />
+    </test>
   </tests>
   <help>
 **What it does**