# HG changeset patch
# User timpalpant
# Date 1339787253 14400
# Node ID b2a69d34385aec30de5601600fa23b373f8e465d
# Parent  ace7855c10172f6055e7550c7fa4fe35d4bd6ab6
Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.

diff -r ace7855c1017 -r b2a69d34385a dist/java-genomics-toolkit.jar
Binary file dist/java-genomics-toolkit.jar has changed
diff -r ace7855c1017 -r b2a69d34385a galaxy-conf/._IntervalToBed.xml
Binary file galaxy-conf/._IntervalToBed.xml has changed
diff -r ace7855c1017 -r b2a69d34385a galaxy-conf/._IntervalToWig.xml
Binary file galaxy-conf/._IntervalToWig.xml has changed
diff -r ace7855c1017 -r b2a69d34385a galaxy-conf/._PredictFAIRESignal.xml
Binary file galaxy-conf/._PredictFAIRESignal.xml has changed
diff -r ace7855c1017 -r b2a69d34385a galaxy-conf/IntervalToBed.xml
--- a/galaxy-conf/IntervalToBed.xml	Sat Jun 09 16:10:42 2012 -0400
+++ b/galaxy-conf/IntervalToBed.xml	Fri Jun 15 15:07:33 2012 -0400
@@ -1,15 +1,19 @@
-<tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed to Bed" version="1.0.0">
+<tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed/VCF to Bed" version="1.0.0">
   <description>converter</description>
   <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command>
   <inputs>
-      <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph" label="Input" />
+      <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph,vcf" label="Input" />
   </inputs>
   <outputs>
       <data name="output" format="bed" metadata_source="input" />
   </outputs>
 <help>
 
-This tool will convert any file in SAM, BAM, GFF, BedGraph, or BigBed format to Bed format.
+This tool will convert any file in SAM, BAM, GFF, BedGraph, BigBed, or VCF format to Bed format.
+
+.. class:: warningmark
+	
+For SAM/BAM data, paired-end reads are converted to Bed format as the entire fragment (5' end of mate 1 to the 5' end of mate 2). Single-end reads are converted to Bed format as the read itself, with strand information. If your SAM/BAM file contains both mate alignments from a paired-end sequencing run (i.e. two entries for each fragment), you should first filter out reads from either the + or - strand with the SAM Tools -> Filter SAM tool to avoid producing redundant entries in the output Bed file.
 
 </help>
 </tool>
diff -r ace7855c1017 -r b2a69d34385a galaxy-conf/IntervalToWig.xml
--- a/galaxy-conf/IntervalToWig.xml	Sat Jun 09 16:10:42 2012 -0400
+++ b/galaxy-conf/IntervalToWig.xml	Fri Jun 15 15:07:33 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="BedToWig" name="Interval to Wig" version="1.1.0">
+<tool id="BedToWig" name="Bed/BedGraph/GFF to Wig" version="1.1.0">
   <description>converter</description>
   <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToWig -i $input $zero -a ${chromInfo} -o $output</command>
   <inputs>
diff -r ace7855c1017 -r b2a69d34385a galaxy-conf/PairOverlappingNucleosomes.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/PairOverlappingNucleosomes.xml	Fri Jun 15 15:07:33 2012 -0400
@@ -0,0 +1,18 @@
+<tool id="PairNukes" name="Pair nucleosomes" version="1.0.0">
+  <description>by overlap</description>
+  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PairOverlappingNucleosomes -a $input1 -b $input2 -m $N -o $output</command>
+  <inputs>
+      <param name="input1" type="data" format="tabular" label="Nucleosome calls 1" />
+      <param name="input2" type="data" format="tabular" label="Nucleosome calls 2" />
+      <param name="N" type="integer" value="73" label="Minimum overlap (bp)" />
+  </inputs>
+  <outputs>
+      <data name="output" format="tabular" />
+  </outputs>
+  
+<help>
+  
+This tool will pair overlapping nucleosomes from two sets of nucleosome calls. In the event that multiple calls overlap, the one with the largest overlap is selected as a match.
+
+</help>
+</tool>
diff -r ace7855c1017 -r b2a69d34385a galaxy-conf/PredictFAIRESignal.xml
--- a/galaxy-conf/PredictFAIRESignal.xml	Sat Jun 09 16:10:42 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-<tool id="PredictFAIRE" name="Predict FAIRE signal" version="1.1.0">
-  <description>from nucleosome occupancy</description>
-  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PredictFAIRESignal -i $input -s $sonication -c $crosslinking -x $extend -o $output</command>
-  <inputs>
-      <param format="bigwig,wig" name="input" type="data" label="Nucleosome occupancy data" />
-      <param format="tabular" name="sonication" type="data" label="Sonication fragment length distribution" />
-      <param name="crosslinking" type="float" value="1.0" label="Crosslinking coefficient" />
-      <param name="extend" type="integer" value="250" label="In silico read extension (-1 for paired-end mode)" />
-  </inputs>
-  <outputs>
-      <data format="wig" name="output" metadata_source="input" />
-  </outputs>
-  
-  <help>
-    
-This tool attempts to predict FAIRE signal from nucleosome occupancy by calculating the probability that a random sonicated fragment is occupied anywhere by a nucleosome.
-
------
-
-**Syntax**
-
-- **Nucleosome occupancy data** should be fragment coverage data from an MNase-seq experiment
-- **Sonication fragment length distribution:** The relative proportion of each size of fragment produced by sonication
-- **Crosslinking coefficient** is the efficiency of crosslinking (what fraction of the time is a nucleosome crosslinked)
-- **In silico read extension** is the length that single-end reads should be extended to match FAIRE-seq data
-
------
-
-Sonication fragment distribution must be provided in the following tabular format ::
-
-  length  proportion
-  
-So for example ::
-
-  1  0.1
-  2  0.2
-  3  0.3
-  4  0.2
-  5  0.2
-    
-  </help>
-</tool>
diff -r ace7855c1017 -r b2a69d34385a lib/java-genomics-io.jar
Binary file lib/java-genomics-io.jar has changed