Mercurial > repos > timpalpant > java_genomics_toolkit

diff galaxy-conf/IntervalToBed.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
children b2a69d34385a
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/IntervalToBed.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -0,0 +1,15 @@
+<tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed to Bed" version="1.0.0">
+  <description>converter</description>
+  <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command>
+  <inputs>
+      <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph" label="Input" />
+  </inputs>
+  <outputs>
+      <data name="output" format="bed" metadata_source="input" />
+  </outputs>
+<help>
+
+This tool will convert any file in SAM, BAM, GFF, BedGraph, or BigBed format to Bed format.
+
+</help>
+</tool>