Mercurial > repos > timpalpant > java_genomics_toolkit

diff galaxy-conf/IntervalToWig.xml @ 20:9d56b5b85740 draft

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Reuploaded to see if tools get loaded correctly this time.
author timpalpant
date Fri, 15 Jun 2012 15:10:26 -0400
parents
children b43c420a6135
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/IntervalToWig.xml	Fri Jun 15 15:10:26 2012 -0400
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+<tool id="BedToWig" name="Bed/BedGraph/GFF to Wig" version="1.1.0">
+  <description>converter</description>
+  <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToWig -i $input $zero -a ${chromInfo} -o $output</command>
+  <inputs>
+      <param name="input" type="data" format="bed,bedgraph,gff" label="Input Bed/BedGraph/GFF file" />
+  	  <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" />
+  </inputs>
+  <outputs>
+      <data name="output" format="wig" metadata_source="input" />
+  </outputs>
+	
+<help>
+
+This tool converts data from an interval format, such as Bed, BedGraph or GFF, to Wig format. This can be used to convert data from microarrays to Wig format. The value of each interval is mapped into the Wig file. Intervals that overlap in the original file (multiple-valued base pairs) are averaged, and bases without data in the original interval file are set to NaN.
+
+.. class:: warningmark
+	
+This tool requires Bed, BedGraph, or GFF formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.
+
+</help>
+</tool>