# HG changeset patch
# User greg
# Date 1449090797 18000
# Node ID 24a8165055bde5ac78c642a6e5e8775f49aa8865
# Parent  962b0366a9800742ea3d102f2fec51c7d751abed
Uploaded

diff -r 962b0366a980 -r 24a8165055bd bam_to_scidx.xml
--- a/bam_to_scidx.xml	Tue Nov 24 08:13:56 2015 -0500
+++ b/bam_to_scidx.xml	Wed Dec 02 16:13:17 2015 -0500
@@ -25,16 +25,18 @@
         <test>
             <param name="input" value="input.bam" ftype="bam" />
             <param name="read" value="0" />
-            <output name="output" file="output.scidx" />
+            <output name="output" file="output.scidx" lines_diff="1" />
         </test>
     </tests>
     <help>
 
 **What it does**
 
-Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by
-tools within the Chip-exo Galaxy flavor.  The Chip-exo Galaxy flavor is used by the Center for
-Eukaryotic Gene Regulation labs at The Pennsylvania State University.  ScIdx files are 1-based.
+Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by tools within
+the Chip-exo Galaxy flavor.  ScIdx files are 1-based.  The format consists of 5 columns: the chromosome,
+the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on
+the reverse strand and the number of total tags on the position.  With pair-end reads, only the 5’ end of
+READ1 will be used to create the ScIdx data file.  Tools that use this format include GeneTrack and MultiGPS.
 
     </help>
     <citations>