# HG changeset patch
# User greg
# Date 1450286547 18000
# Node ID cd105fdfb0da705fc5f2573602afbed88b1c72f2
# Parent  497e3274f70ba976f0fc0883bac6e5058a11ec81
Uploaded

diff -r 497e3274f70b -r cd105fdfb0da genetrack.xml
--- a/genetrack.xml	Wed Dec 02 16:15:05 2015 -0500
+++ b/genetrack.xml	Wed Dec 16 12:22:27 2015 -0500
@@ -38,8 +38,8 @@
         </conditional>
         <param name="sigma" type="integer" value="5" min="1" label="Sigma to use when smoothing reads" help="Higher values increase computation but produce more smoothing." />
         <param name="exclusion" type="integer" value="20" min="1" label="Peak exclusion zone" help="Exclusion zone around each peak that prevents others from being called." />
-        <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="up_width" type="integer" value="10" min="0" label="Exclusion zone of upstream called peaks" />
+        <param name="down_width" type="integer" value="10" min="0" label="Exclusion zone of downstream called peaks" />
         <param name="filter" type="integer" value="3" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." />
     </inputs>
     <outputs>
@@ -88,22 +88,32 @@
     <help>
 **What it does**
 
-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.
+<![CDATA[
+
+GeneTrack separately identifies peaks on the forward "+” and reverse “-” strand.  The way that GeneTrack works
+is to replace each tag with a probabilistic distribution of occurrences for that tag at and around its mapped
+genomic coordinate.  The distance decay of the probabilistic distribution is set by adjusting the value of the
+tool's **Sigma to use when smoothing reads** parameter.  GeneTrack then sums the distribution over all mapped
+tags.  This results in a smooth continuous trace that can be globally broadened or tightened by adjusting the
+sigma value.  GeneTrack starts with the highest smoothed peak first, treating each strand separately if indicated
+by the data, then sets up an exclusion zone (centered over the peak) defined by the value of the **Peak exclusion
+zone** parameter (see figure).  The exclusion zone prevents any secondary peaks from being called on the same strand
+within that exclusion zone.  In rare cases, it may be desirable to set different exclusion zones upstream (more 5’)
+versus downstream (more 3’) of the peak.
+
+]]>
+
+.. image:: $PATH_TO_IMAGES/genetrack.png
 
 -----
 
 **Options**
 
-* **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks.
-* **Peak exclusion zone** - Exclusion zone around each peak that prevents others from being called.
-* **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.
+* **Sigma to use when smoothing reads** - Smooths clusters of tags via a Gaussian distribution.
+* **Peak exclusion zone** - Exclusion zone around each peak, eliminating all other peaks on the same strand that are within a ± bp distance of the peak.
+* **Exclusion zone of upstream called peaks** - Defines the exclusion zone centered over peaks upstream of a peak.
+* **Exclusion zone of downstream called peaks** - Defines the exclusion zone centered over peaks downstream of a peak.
+* **Filter** - Absolute read filter, restricts output to only peaks with larger peak height.
     </help>
     <expand macro="citations" />
 </tool>
diff -r 497e3274f70b -r cd105fdfb0da static/images/._genetrack.png
Binary file static/images/._genetrack.png has changed
diff -r 497e3274f70b -r cd105fdfb0da static/images/genetrack.png
Binary file static/images/genetrack.png has changed
diff -r 497e3274f70b -r cd105fdfb0da test-data/genetrack_input3.scidx
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genetrack_input3.scidx	Wed Dec 16 12:22:27 2015 -0500
@@ -0,0 +1,100 @@
+chrom	index	forward	reverse	value
+chr01	7	2	0	2
+chr01	8	3	0	3
+chr01	10	2	0	2
+chr01	14	1	0	1
+chr01	15	1	0	1
+chr01	16	1	0	1
+chr01	31	1	0	1
+chr01	32	1	0	1
+chr01	35	1	0	1
+chr01	37	2	0	2
+chr01	38	65	0	65
+chr01	39	8	4	12
+chr01	40	3	0	3
+chr01	41	3	2	5
+chr01	42	3	1	4
+chr01	43	2	2	4
+chr01	44	0	1	1
+chr01	46	3	0	3
+chr01	52	0	1	1
+chr01	54	7	0	7
+chr01	55	2	0	2
+chr01	56	1	0	1
+chr01	58	0	1	1
+chr01	61	0	1	1
+chr01	62	1	3	4
+chr01	63	0	1	1
+chr01	64	2	4	6
+chr01	66	0	13	13
+chr01	67	0	4	4
+chr01	72	0	5	5
+chr01	75	4	0	4
+chr01	77	0	6	6
+chr01	81	13	0	13
+chr01	83	1	0	1
+chr01	85	0	4	4
+chr01	86	0	1	1
+chr01	89	4	0	4
+chr01	90	1	0	1
+chr01	91	2	0	2
+chr01	92	4	1	5
+chr01	93	4	0	4
+chr01	96	1	0	1
+chr01	97	1	0	1
+chr01	98	4	0	4
+chr01	99	8	0	8
+chr01	102	1	1	2
+chr01	105	0	1	1
+chr01	107	0	3	3
+chr01	109	0	4	4
+chr01	110	2	1	3
+chr01	111	6	0	6
+chr01	112	0	3	3
+chr01	113	24	0	24
+chr01	114	0	32	32
+chr01	115	5	4	9
+chr01	116	36	5	41
+chr01	117	194	5	199
+chr01	118	100	2	102
+chr01	119	98	19	117
+chr01	120	92	7	99
+chr01	121	112	11	123
+chr01	122	36	3	39
+chr01	123	18	16	34
+chr01	124	9	14	23
+chr01	125	14	12	26
+chr01	126	20	1	21
+chr01	127	4	2	6
+chr01	128	66	6	72
+chr01	129	3	6	9
+chr01	130	2	10	12
+chr01	131	62	0	62
+chr01	132	20	1	21
+chr01	133	64	1	65
+chr01	134	58	0	58
+chr01	135	83	4	87
+chr01	136	92	1	93
+chr01	137	12	0	12
+chr01	138	0	3	3
+chr01	139	0	2	2
+chr01	142	0	48	48
+chr01	143	0	15	15
+chr01	144	0	74	74
+chr01	145	23	11	34
+chr01	146	1	120	121
+chr01	147	0	574	574
+chr01	148	0	11	11
+chr01	150	1	0	1
+chr01	151	3	4	7
+chr01	152	0	2	2
+chr01	153	1	3	4
+chr01	155	8	11	19
+chr01	156	0	14	14
+chr01	158	0	3	3
+chr01	159	0	1	1
+chr01	160	0	1	1
+chr01	161	0	5	5
+chr01	163	0	2	2
+chr01	164	0	29	29
+chr01	165	0	1	1
diff -r 497e3274f70b -r cd105fdfb0da test-data/genetrack_input3.ssccidx
--- a/test-data/genetrack_input3.ssccidx	Wed Dec 02 16:15:05 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-chrom	index	forward	reverse	value
-chr01	7	2	0	2
-chr01	8	3	0	3
-chr01	10	2	0	2
-chr01	14	1	0	1
-chr01	15	1	0	1
-chr01	16	1	0	1
-chr01	31	1	0	1
-chr01	32	1	0	1
-chr01	35	1	0	1
-chr01	37	2	0	2
-chr01	38	65	0	65
-chr01	39	8	4	12
-chr01	40	3	0	3
-chr01	41	3	2	5
-chr01	42	3	1	4
-chr01	43	2	2	4
-chr01	44	0	1	1
-chr01	46	3	0	3
-chr01	52	0	1	1
-chr01	54	7	0	7
-chr01	55	2	0	2
-chr01	56	1	0	1
-chr01	58	0	1	1
-chr01	61	0	1	1
-chr01	62	1	3	4
-chr01	63	0	1	1
-chr01	64	2	4	6
-chr01	66	0	13	13
-chr01	67	0	4	4
-chr01	72	0	5	5
-chr01	75	4	0	4
-chr01	77	0	6	6
-chr01	81	13	0	13
-chr01	83	1	0	1
-chr01	85	0	4	4
-chr01	86	0	1	1
-chr01	89	4	0	4
-chr01	90	1	0	1
-chr01	91	2	0	2
-chr01	92	4	1	5
-chr01	93	4	0	4
-chr01	96	1	0	1
-chr01	97	1	0	1
-chr01	98	4	0	4
-chr01	99	8	0	8
-chr01	102	1	1	2
-chr01	105	0	1	1
-chr01	107	0	3	3
-chr01	109	0	4	4
-chr01	110	2	1	3
-chr01	111	6	0	6
-chr01	112	0	3	3
-chr01	113	24	0	24
-chr01	114	0	32	32
-chr01	115	5	4	9
-chr01	116	36	5	41
-chr01	117	194	5	199
-chr01	118	100	2	102
-chr01	119	98	19	117
-chr01	120	92	7	99
-chr01	121	112	11	123
-chr01	122	36	3	39
-chr01	123	18	16	34
-chr01	124	9	14	23
-chr01	125	14	12	26
-chr01	126	20	1	21
-chr01	127	4	2	6
-chr01	128	66	6	72
-chr01	129	3	6	9
-chr01	130	2	10	12
-chr01	131	62	0	62
-chr01	132	20	1	21
-chr01	133	64	1	65
-chr01	134	58	0	58
-chr01	135	83	4	87
-chr01	136	92	1	93
-chr01	137	12	0	12
-chr01	138	0	3	3
-chr01	139	0	2	2
-chr01	142	0	48	48
-chr01	143	0	15	15
-chr01	144	0	74	74
-chr01	145	23	11	34
-chr01	146	1	120	121
-chr01	147	0	574	574
-chr01	148	0	11	11
-chr01	150	1	0	1
-chr01	151	3	4	7
-chr01	152	0	2	2
-chr01	153	1	3	4
-chr01	155	8	11	19
-chr01	156	0	14	14
-chr01	158	0	3	3
-chr01	159	0	1	1
-chr01	160	0	1	1
-chr01	161	0	5	5
-chr01	163	0	2	2
-chr01	164	0	29	29
-chr01	165	0	1	1
diff -r 497e3274f70b -r cd105fdfb0da tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 02 16:15:05 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 16 12:22:27 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="anaconda" version="2.3.0">
-        <repository changeset_revision="1da77309352e" name="package_anaconda_2_3_0" owner="greg" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="d3f29b11da06" name="package_anaconda_2_3_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>