Mercurial > repos > timpalpant > java_genomics_toolkit

diff galaxy-conf/RollingReadLength.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/RollingReadLength.xml	Fri Jun 15 15:10:26 2012 -0400
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+<tool id="RollingReadLength" name="Compute mean fragment length" version="1.1.0">
+  <description>over each locus</description>
+  <command interpreter="sh">galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output</command>
+  <inputs>
+      <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" />
+  </inputs>
+  <outputs>
+      <data format="wig" name="output" />
+  </outputs>
+  
+<help>
+  
+This tool will compute the mean length of all fragments overlapping a given locus, and can be used to identify sites with exceptionally long or short reads.
+  
+.. class:: warningmark
+
+This tool requires paired-end SAM, BAM, Bed, or BedGraph formatted data. Using single-end data will result in a constant read length.
+
+</help>
+</tool>