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

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/Downsample.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/Downsample.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="WigDownsample" name="Downsample" version="1.0.0">
+<tool id="WigDownsample" name="Downsample" version="1.1.0">
   <description>a (Big)Wig file</description>
   <command interpreter="sh">galaxyToolRunner.sh wigmath.Downsample -i $input -m $metric -w $window -o $output</command>
   <inputs>
@@ -16,6 +16,27 @@
       <data format="wig" name="output" metadata_source="input" />
   </outputs>
   
+  <tests>
+      <test>
+	    <param name="input" value="wigmath1.wig"/>
+	    <param name="window" value="1"/>
+	    <param name="metric" value="mean"/>
+	    <output name="output" file="downsample1.wig"/>
+	  </test>
+	  <test>
+	    <param name="input" value="wigmath2.bw"/>
+	    <param name="window" value="5"/>
+	    <param name="metric" value="max"/>
+	    <output name="output" file="downsample2.wig"/>
+	  </test>
+	  <test>
+	    <param name="input" value="wigmath3.wig"/>
+	    <param name="window" value="100"/>
+	    <param name="metric" value="total"/>
+	    <output name="output" file="downsample3.wig"/>
+	  </test>
+  </tests>
+  
   <help>
 
 This tool can be used to reduce the resolution and file size of Wig files for easier upload to UCSC. Data is downsampled in non-overlapping windows starting from the beginning of each chromosome. Each window can be downsampled as the mean, minimum, maximum, total, or coverage of the original data.