Mercurial > repos > timpalpant > java_genomics_toolkit

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 b43c420a6135
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/ExtractDataFromRegion.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -0,0 +1,27 @@
+<tool id="ExtractDataFromWig" name="Extract data from a Wig file" version="1.0.0">
+  <description>for a genomic interval</description>
+  <command interpreter="sh">
+  	galaxyToolRunner.sh ngs.ExtractDataFromRegion --chr $chr --start $start --stop $stop -o $output $file1
+  	  #for $input in $inputs
+        ${input.file}
+      #end for
+  </command>
+  <inputs>
+  	  <param name="file1" label="(Big)Wig file" type="data" format="bigwig,wig" />
+      <repeat name="inputs" title="(Big)Wig file">
+        <param name="file" type="data" format="bigwig,wig" />
+      </repeat>
+      <param name="chr" type="text" label="Chromosome" />
+      <param name="start" type="integer" value="1" label="Start base pair" />
+      <param name="stop" type="integer" value="1000" label="Stop base pair" />
+  </inputs>
+  <outputs>
+      <data format="tabular" name="output" />
+  </outputs>
+  
+<help>
+  
+This tool will extract data from Wig or BigWig file(s) for a specific region of the genome.
+
+</help>
+</tool>