Mercurial > repos > timpalpant > java_genomics_toolkit

diff galaxy-conf/FindNMers.xml @ 15:3e477c7e0e73 draft

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Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
author timpalpant
date Sat, 09 Jun 2012 16:03:59 -0400
parents eb53be9a09f4
children
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--- a/galaxy-conf/FindNMers.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/FindNMers.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -34,10 +34,19 @@
   <outputs>
       <data format="bed" name="output"/>
   </outputs>
+  <tests>
+    <test>
+      <param name="genomeSource" value="history"/>
+      <param name="ownFile" value="test.fasta"/>
+      <param name="property" value="Twist"/>
+      <param name="N" value="false"/>
+      <output name="output" file="twist.wig"/>
+  	</test>
+	</tests>
   
   <help>
 
-This tool will find all matches of a given NMer in a DNA sequence.
+This tool will find all matches of a given NMer in a DNA sequence. Sequences may be provided in FASTA format or selected from available reference genomes. Mismatches are allowed, but not insertions/deletions. The output is a Bed file with the locations of matches in the reference sequence.
 
   </help>
 </tool>