# HG changeset patch
# User greg
# Date 1449090905 18000
# Node ID 497e3274f70ba976f0fc0883bac6e5058a11ec81
# Parent  1a9f1a4fa36cfad9c4056bdaf823fc16a9a141b4
Uploaded

diff -r 1a9f1a4fa36c -r 497e3274f70b genetrack.xml
--- a/genetrack.xml	Wed Dec 02 16:14:58 2015 -0500
+++ b/genetrack.xml	Wed Dec 02 16:15:05 2015 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="genetrack" name="Genetrack" version="@WRAPPER_VERSION@.0">
+<tool id="genetrack" name="GeneTrack" version="@WRAPPER_VERSION@.0">
     <description>peak predictor</description>
     <macros>
         <import>genetrack_macros.xml</import>
@@ -22,7 +22,6 @@
         --up_width $up_width
         --down_width $down_width
         --filter $filter
-        --chunk_size $chunk_size
     </command>
     <inputs>
         <conditional name="input_format_cond">
@@ -42,7 +41,6 @@
         <param name="up_width" type="integer" value="10" min="0" label="Upstream width of called peaks" />
         <param name="down_width" type="integer" value="10" min="0" label="Downstream width of called peaks" />
         <param name="filter" type="integer" value="3" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." />
-        <param name="chunk_size" type="integer" value="10" min="1" label="Chunk each chromosome into" help="Value is millions of base pairs where each size increment uses about 20MB of memory." />
     </inputs>
     <outputs>
         <collection name="genetrack_output" type="list" label="Genetrack results on ${on_string}">
@@ -58,7 +56,6 @@
             <param name="up_width" value="10" />
             <param name="down_width" value="10" />
             <param name="filter" value="3" />
-            <param name="chunk_size" value="10" />
             <output_collection name="genetrack_output" type="list">
                 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output2.gff" ftype="gff" />
             </output_collection>
@@ -71,7 +68,6 @@
             <param name="up_width" value="10" />
             <param name="down_width" value="10" />
             <param name="filter" value="3" />
-            <param name="chunk_size" value="10" />
             <output_collection name="genetrack_output" type="list">
                 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output3.gff" ftype="gff" />
             </output_collection>
@@ -84,7 +80,6 @@
             <param name="up_width" value="10" />
             <param name="down_width" value="10" />
             <param name="filter" value="3" />
-            <param name="chunk_size" value="10" />
             <output_collection name="genetrack_output" type="list">
                 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output4.gff" ftype="gff" />
             </output_collection>
@@ -93,9 +88,11 @@
     <help>
 **What it does**
 
-Genetrack takes a standard set of data on both the sense and antisense strands and smooths their relative reads.
-It then calls the peaks present in the smoothed dataset and uses those peak locations to calculate the final
-reads from surrounding reads.  Finally, it ensures each peak is above a threshold and that two peaks are not
+Genetrack supports ChIP experiments.  The peak caller takes a standard set of data on both the sense and
+antisense strands (ScIdx format) and smooths their relative reads. It then predicts the peaks present in
+the smoothed dataset and uses those peak locations to find the maximal non-overlapping subset.  It then
+selects the highest peak and establishes an exclusion zone, and no other predicted peaks will be reported
+within the exclusion zone.  Finally, it ensures each peak is above a threshold and that two peaks are not
 too close to each other.
 
 -----
@@ -107,7 +104,6 @@
 * **Upstream width of called peaks** - Upstream width of called peaks.
 * **Downstream width of called peaks** - Downstream width of called peaks.
 * **Filter** - Absolute read filter.  Restricts output to only peaks with larger peak height.
-* **Chunk each chromosome into** - Size, in millions of base pairs, to chunk each chromosome when processing.  Each 1 million size uses approximately 20MB of memory.
     </help>
     <expand macro="citations" />
 </tool>