# HG changeset patch
# User timpalpant
# Date 1339272239 14400
# Node ID 3e477c7e0e73d5533a56afd85d3ff8d39584a1d5
# Parent  f58706d4d4212349d41d7ccec28ee921881f095f
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.

diff -r f58706d4d421 -r 3e477c7e0e73 dist/java-genomics-toolkit.jar
Binary file dist/java-genomics-toolkit.jar has changed
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._Autocorrelation.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._Correlate.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._DNAPropertyCalculator.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._Divide.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._DynaPro.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._FastqIlluminaToSanger.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._FindNMers.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._GaussianSmooth.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._InterpolateDiscontinuousData.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._IntervalLengthDistribution.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._MapDyads.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._MovingAverageSmooth.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._NRLCalculator.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._ReadLengthDistributionMatrix.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._Summary.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._WaveletTransform.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._WigCorrelate.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._WigSummary.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._ZScore.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/._Zinba.xml
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diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Add.xml
--- a/galaxy-conf/Add.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/Add.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="WigAdd" name="Add" version="1.0.0">
+<tool id="WigAdd" name="Add" version="1.1.0">
   <description>multiple (Big)Wig files</description>
   <command interpreter="sh">
     galaxyToolRunner.sh wigmath.Add -o $output
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Average.xml
--- a/galaxy-conf/Average.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/Average.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="WigAvg" name="Average" version="1.0.0">
+<tool id="WigAvg" name="Average" version="1.1.0">
   <description>multiple (Big)Wig files</description>
   <command interpreter="sh">
     galaxyToolRunner.sh wigmath.Average -o $output $file1 $file2
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/BaseAlignCounts.xml
--- a/galaxy-conf/BaseAlignCounts.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/BaseAlignCounts.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="BaseAlignCounts" name="Calculate coverage" version="1.0.0">
+<tool id="BaseAlignCounts" name="Calculate coverage" version="2.0.0">
   <description>of sequencing reads</description>
   <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Correlate.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/Correlate.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -0,0 +1,60 @@
+<tool id="WigCorrelate" name="Correlate" version="1.1.0">
+  <description>multiple (Big)Wig files</description>
+  <command interpreter="sh">
+    galaxyToolRunner.sh wigmath.Correlate -w $window -s $step -t $type -o $output $file1 $file2
+      #for $input in $inputs
+        ${input.file}
+      #end for
+  </command>
+  <inputs>
+      <param name="file1" label="(Big)Wig file 1" type="data" format="bigwig,wig" />
+      <param name="file2" label="(Big)Wig file 2" type="data" format="bigwig,wig" />
+      <repeat name="inputs" title="Additional (Big)Wig file">
+        <param name="file" type="data" format="bigwig,wig" />
+      </repeat>
+      <param name="window" type="integer" value="100" label="Window size (bp)" />
+      <param name="step" type="integer" value="50" label="Sliding step size (bp)" />
+      <param name="type" type="select" label="Correlation metric">
+      	<option value="pearson">Pearson</option>
+      	<option value="spearman">Spearman</option>
+      </param>
+  </inputs>
+  <outputs>
+      <data format="tabular" name="output" />
+  </outputs>
+  
+<help>
+  
+This tool will compute a correlation matrix between the supplied Wig or BigWig files. Each row/column in the matrix is added in the order that files are added above, starting from the top left. The Wig file is downsampled into sliding windows with the specified bin size and shift by computing the mean value in each window. These windows are then correlated using either Pearson_'s Product-Moment correlation coefficient or Spearman_'s rank correlation coefficient. If the window size is set to 1, the correlation is calculated between all base pairs in the genome.
+  
+.. _Pearson: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient
+
+.. _Spearman: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
+  
+-----
+
+**Syntax**
+
+- **Inputs** are the genomic data to correlate
+- **Window size** is the size of the window to bin data into
+- **Sliding step size** is the shift step size of the sliding window used during binning
+- **Correlation metric** is the type of correlation to calculate
+  
+-----
+
+.. class:: warningmark
+
+**WARN:** In order to calculate the correlation coefficient, the data is loaded into entirely into memory. For large genomes, this may require a lot of RAM unless comparably larger window sizes are used.
+
+-----
+
+**Citation**
+
+This tool was inspired by ACT_ from the Gerstein lab.
+
+.. _ACT: http://act.gersteinlab.org
+
+J Jee*, J Rozowsky*, KY Yip*, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein. ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks. (2011) Bioinformatics 27(8): 1152-4.
+  
+</help>
+</tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/DNAPropertyCalculator.xml
--- a/galaxy-conf/DNAPropertyCalculator.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/DNAPropertyCalculator.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="DNAPropertyCalculator" name="Calculate sequence-specific DNA properties" version="1.0.0">
+<tool id="DNAPropertyCalculator" name="Calculate sequence-specific DNA properties" version="2.0.0">
   <description>for a genome</description>
   <command interpreter="sh">galaxyToolRunner.sh dna.DNAPropertyCalculator -i 
     #if $refGenomeSource.genomeSource == "history":
@@ -85,12 +85,14 @@
     <test>
       <param name="genomeSource" value="history"/>
       <param name="ownFile" value="test.fasta"/>
+      <param name="property" value="Twist"/>
       <param name="N" value="false"/>
       <output name="output" file="twist.wig"/>
   	</test>
   	<test>
       <param name="genomeSource" value="history"/>
       <param name="ownFile" value="test.fasta"/>
+      <param name="property" value="Twist"/>
       <param name="N" value="true"/>
       <output name="output" file="twist.normalized.wig"/>
   	</test>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Divide.xml
--- a/galaxy-conf/Divide.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/Divide.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="Divide" name="Divide" version="1.0.0">
+<tool id="WigDivide" name="Divide" version="1.1.0">
   <description>two (Big)Wig files</description>
   <command interpreter="sh">galaxyToolRunner.sh wigmath.Divide -n $dividend -d $divisor -o $output</command>
   <inputs>
@@ -9,30 +9,21 @@
     <data format="wig" name="output" metadata_source="dividend" />
   </outputs>
   <tests>
-    <!--<test>
-	    <param name="dividend" value="wigmath.input1"/>
-	    <param name="divisor" value="wigmath.input2"/>
-	    <param name="dbkey" value="sacCer2"/>
-	    <output name="output" file="divide.output"/>
+      <test>
+	    <param name="dividend" value="wigmath1.wig"/>
+	    <param name="divisor" value="wigmath2.wig"/>
+	    <output name="output" file="divide1.wig"/>
 	  </test>
 	  <test>
-	    <param name="dividend" value="wigmath.input1.bw"/>
-	    <param name="divisor" value="wigmath.input2"/>
-	    <param name="dbkey" value="sacCer2"/>
-	    <output name="output" file="divide.output"/>
+	    <param name="dividend" value="wigmath1.wig"/>
+	    <param name="divisor" value="wigmath3.bw"/>
+	    <output name="output" file="divide2.wig"/>
 	  </test>
 	  <test>
-	    <param name="dividend" value="wigmath.input1"/>
-	    <param name="divisor" value="wigmath.input2.bw"/>
-	    <param name="dbkey" value="sacCer2"/>
-	    <output name="output" file="divide.output"/>
+	    <param name="dividend" value="wigmath3.bw"/>
+	    <param name="divisor" value="wigmath2.bw"/>
+	    <output name="output" file="divide3.wig"/>
 	  </test>
-	  <test>
-	    <param name="dividend" value="wigmath.input1.bw"/>
-	    <param name="divisor" value="wigmath.input2.bw"/>
-	    <param name="dbkey" value="sacCer2"/>
-	    <output name="output" file="divide.output"/>
-	  </test>-->
   </tests>
   
   <help>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Downsample.xml
--- a/galaxy-conf/Downsample.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/Downsample.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="WigDownsample" name="Downsample" version="1.0.0">
+<tool id="WigDownsample" name="Downsample" version="1.1.0">
   <description>a (Big)Wig file</description>
   <command interpreter="sh">galaxyToolRunner.sh wigmath.Downsample -i $input -m $metric -w $window -o $output</command>
   <inputs>
@@ -16,6 +16,27 @@
       <data format="wig" name="output" metadata_source="input" />
   </outputs>
   
+  <tests>
+      <test>
+	    <param name="input" value="wigmath1.wig"/>
+	    <param name="window" value="1"/>
+	    <param name="metric" value="mean"/>
+	    <output name="output" file="downsample1.wig"/>
+	  </test>
+	  <test>
+	    <param name="input" value="wigmath2.bw"/>
+	    <param name="window" value="5"/>
+	    <param name="metric" value="max"/>
+	    <output name="output" file="downsample2.wig"/>
+	  </test>
+	  <test>
+	    <param name="input" value="wigmath3.wig"/>
+	    <param name="window" value="100"/>
+	    <param name="metric" value="total"/>
+	    <output name="output" file="downsample3.wig"/>
+	  </test>
+  </tests>
+  
   <help>
 
 This tool can be used to reduce the resolution and file size of Wig files for easier upload to UCSC. Data is downsampled in non-overlapping windows starting from the beginning of each chromosome. Each window can be downsampled as the mean, minimum, maximum, total, or coverage of the original data.
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/DynaPro.xml
--- a/galaxy-conf/DynaPro.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/DynaPro.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="DynaPro" name="Compute equilibrium nucleosome positions" version="1.0.0">
+<tool id="DynaPro" name="Compute equilibrium nucleosome positions" version="1.1.0">
   <description>using DynaPro</description>
   <command interpreter="sh">galaxyToolRunner.sh nucleosomes.DynaPro -i $input -n $N 
     #if str( $mean ) != ''
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/ExtractDataFromRegion.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/ExtractDataFromRegion.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -0,0 +1,27 @@
+<tool id="ExtractDataFromWig" name="Extract data from a Wig file" version="1.0.0">
+  <description>for a genomic interval</description>
+  <command interpreter="sh">
+  	galaxyToolRunner.sh ngs.ExtractDataFromRegion --chr $chr --start $start --stop $stop -o $output $file1
+  	  #for $input in $inputs
+        ${input.file}
+      #end for
+  </command>
+  <inputs>
+  	  <param name="file1" label="(Big)Wig file" type="data" format="bigwig,wig" />
+      <repeat name="inputs" title="(Big)Wig file">
+        <param name="file" type="data" format="bigwig,wig" />
+      </repeat>
+      <param name="chr" type="text" label="Chromosome" />
+      <param name="start" type="integer" value="1" label="Start base pair" />
+      <param name="stop" type="integer" value="1000" label="Stop base pair" />
+  </inputs>
+  <outputs>
+      <data format="tabular" name="output" />
+  </outputs>
+  
+<help>
+  
+This tool will extract data from Wig or BigWig file(s) for a specific region of the genome.
+
+</help>
+</tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/FastqIlluminaToSanger.xml
--- a/galaxy-conf/FastqIlluminaToSanger.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/FastqIlluminaToSanger.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -15,11 +15,15 @@
   </tests>
 <help>
 
-This tool will convert a FASTQ file with ASCII quality scores encoded in Illumina 1.3 format (Phred+64) to Sanger format (Phred+33). It is a simpler, faster version of the FASTQ Groomer.
+This tool will convert a FASTQ file with ASCII quality scores encoded in Illumina 1.3-1.7 format (Phred+64) to Sanger format (Phred+33) for use with Bowtie and other Galaxy tools. Illumina CASAVA >= 1.8 already produces FASTQ files in Sanger format, so this tool should not be used on new Illumina sequencing data. This tool is a simpler, faster version of the FASTQ Groomer that does little error checking but performs much faster. If you are unsure what format your file is in, or need to do other conversions, use the FASTQ Groomer instead.
+
+For more information, read about FASTQ formats_ (right-click to open in new window).
+
+.. _formats: http://en.wikipedia.org/wiki/FASTQ_format
 
 .. class:: warningmark
 	
-This tool requires fastqillumina formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.
+This tool requires fastqillumina formatted data. If you have fastq data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.
 
 </help>
 </tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/FindAbsoluteMaxima.xml
--- a/galaxy-conf/FindAbsoluteMaxima.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/FindAbsoluteMaxima.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="FindWigMaxima" name="Find absolute maxima" version="1.0.0">
+<tool id="FindWigMaxima" name="Find absolute maxima" version="1.1.0">
   <description>in intervals</description>
   <command interpreter="sh">
     galaxyToolRunner.sh ngs.FindAbsoluteMaxima -l $window -o $output
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/FindBoundaryNucleosomes.xml
--- a/galaxy-conf/FindBoundaryNucleosomes.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/FindBoundaryNucleosomes.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="FindNuke" name="Find boundary nucleosomes" version="1.0.0">
+<tool id="FindNuke" name="Find boundary nucleosomes" version="2.0.0">
   <description>in windows</description>
   <command interpreter="sh">galaxyToolRunner.sh nucleosomes.FindBoundaryNucleosomes -i $input -l $loci -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/FindNMers.xml
--- a/galaxy-conf/FindNMers.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/FindNMers.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -34,10 +34,19 @@
   <outputs>
       <data format="bed" name="output"/>
   </outputs>
+  <tests>
+    <test>
+      <param name="genomeSource" value="history"/>
+      <param name="ownFile" value="test.fasta"/>
+      <param name="property" value="Twist"/>
+      <param name="N" value="false"/>
+      <output name="output" file="twist.wig"/>
+  	</test>
+	</tests>
   
   <help>
 
-This tool will find all matches of a given NMer in a DNA sequence.
+This tool will find all matches of a given NMer in a DNA sequence. Sequences may be provided in FASTA format or selected from available reference genomes. Mismatches are allowed, but not insertions/deletions. The output is a Bed file with the locations of matches in the reference sequence.
 
   </help>
 </tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/FindOutlierRegions.xml
--- a/galaxy-conf/FindOutlierRegions.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/FindOutlierRegions.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="WigFindOutliers" name="Find outlier regions" version="1.0.0">
+<tool id="WigFindOutliers" name="Find outlier regions" version="1.1.0">
   <description>such as CNVs</description>
   <command interpreter="sh">galaxyToolRunner.sh ngs.FindOutlierRegions -i $input -w $window -t $threshold $below -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/GaussianSmooth.xml
--- a/galaxy-conf/GaussianSmooth.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/GaussianSmooth.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="GaussianSmoother" name="Gaussian smooth" version="1.0.0">
+<tool id="WigGaussianSmooth" name="Gaussian smooth" version="1.1.0">
   <description>a (Big)Wig file</description>
   <command interpreter="sh">galaxyToolRunner.sh wigmath.GaussianSmooth -i $input -s $S -o $output</command>
   <inputs>
@@ -9,48 +9,21 @@
       <data format="wig" name="output" metadata_source="input" />
   </outputs>
   <tests>
-    <!--<test>
-	    <param name="input" value="test.wig"/>
-	    <param name="dbkey" value="sacCer2"/>
+    <test>
+	    <param name="input" value="wigmath1.wig"/>
 	    <param name="S" value="20"/>
-	    <param name="W" value="3"/>
-	    <output name="output" file="smoother.output1"/>
-	  </test>
-	  <test>
-	    <param name="input" value="test.bw"/>
-	    <param name="dbkey" value="sacCer2"/>
-	    <param name="S" value="20"/>
-	    <param name="W" value="3"/>
-	    <output name="output" file="smoother.output1"/>
+	    <output name="output" file="gaussian1.wig"/>
 	  </test>
 	  <test>
-	    <param name="input" value="test.wig"/>
-	    <param name="dbkey" value="sacCer2"/>
-	    <param name="S" value="10"/>
-	    <param name="W" value="2"/>
-	    <output name="output" file="smoother.output2"/>
-	  </test>
-	  <test>
-	    <param name="input" value="test.bw"/>
-	    <param name="dbkey" value="sacCer2"/>
-	    <param name="S" value="10"/>
-	    <param name="W" value="2"/>
-	    <output name="output" file="smoother.output2"/>
+	    <param name="input" value="wigmath2.bw"/>
+	    <param name="S" value="3"/>
+	    <output name="output" file="gaussian2.wig"/>
 	  </test>
 	  <test>
-	    <param name="input" value="test.wig"/>
-	    <param name="dbkey" value="sacCer2"/>
-	    <param name="S" value="50"/>
-	    <param name="W" value="1"/>
-	    <output name="output" file="smoother.output3"/>
+	    <param name="input" value="wigmath3.wig"/>
+	    <param name="S" value="40"/>
+	    <output name="output" file="gaussian3.wig"/>
 	  </test>
-	  <test>
-	    <param name="input" value="test.bw"/>
-	    <param name="dbkey" value="sacCer2"/>
-	    <param name="S" value="5"/>
-	    <param name="W" value="1"/>
-	    <output name="output" file="smoother.output3"/>
-	  </test>-->
   </tests>
   
 <help>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/GeneTrackToBedGraph.xml
--- a/galaxy-conf/GeneTrackToBedGraph.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/GeneTrackToBedGraph.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="GeneTrackToBedGraph" name="GeneTrack to BedGraph" version="1.0.0">
+<tool id="GeneTrackToBedGraph" name="GeneTrack to BedGraph" version="1.1.0">
   <description>converter</description>
   <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToBedGraph -i $input -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/GeneTrackToWig.xml
--- a/galaxy-conf/GeneTrackToWig.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/GeneTrackToWig.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="GeneTrackToWig" name="GeneTrack to Wig" version="1.0.0">
+<tool id="GeneTrackToWig" name="GeneTrack to Wig" version="1.1.0">
   <description>converter</description>
   <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToWig -i $input -s $shift $zero -a ${chromInfo} -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/GreedyCaller.xml
--- a/galaxy-conf/GreedyCaller.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/GreedyCaller.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="CallNukes" name="Call Nucleosomes" version="1.0.0">
+<tool id="CallNukes" name="Call Nucleosomes" version="1.1.0">
   <description>in an MNase experiment</description>
   <command interpreter="sh">galaxyToolRunner.sh nucleosomes.GreedyCaller -d $dyads -s $smoothed -n $N -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/InterpolateDiscontinuousData.xml
--- a/galaxy-conf/InterpolateDiscontinuousData.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/InterpolateDiscontinuousData.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="WigInterpolate" name="Interpolate" version="1.0.0">
+<tool id="WigInterpolate" name="Interpolate" version="1.1.0">
   <description>missing values in a (Big)Wig file</description>
   <command interpreter="sh">galaxyToolRunner.sh converters.InterpolateDiscontinousData -i $input -t $type -m $max -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/IntervalAverager.xml
--- a/galaxy-conf/IntervalAverager.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/IntervalAverager.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="IntervalAverager" name="Average intervals" version="1.0.0">
+<tool id="IntervalAverager" name="Average intervals" version="2.1.0">
   <description>that have been aligned</description>
   <command interpreter="sh">
     galaxyToolRunner.sh visualization.IntervalAverager -l $loci -o $output $file1
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/IntervalLengthDistribution.xml
--- a/galaxy-conf/IntervalLengthDistribution.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/IntervalLengthDistribution.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -8,6 +8,23 @@
   <outputs>
       <data format="tabular" name="output" />
   </outputs>
+  <tests>
+    <test>
+      <param name="input" value="test.bed"/>
+      <param name="freq" value="false"/>
+	    <output name="output" file="intervallengthdistribution1.txt"/>
+    </test>
+    <test>
+      <param name="input" value="test.bed"/>
+      <param name="freq" value="true"/>
+	    <output name="output" file="intervallengthdistribution2.txt"/>
+    </test>
+    <test>
+      <param name="input" value="test2.bed"/>
+      <param name="freq" value="false"/>
+	    <output name="output" file="intervallengthdistribution3.txt"/>
+    </test>
+  </tests>
   
 <help>
   
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/IntervalToBed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/IntervalToBed.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -0,0 +1,15 @@
+<tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed 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" />
+  </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.
+
+</help>
+</tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/IntervalToWig.xml
--- a/galaxy-conf/IntervalToWig.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/IntervalToWig.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="BedToWig" name="Interval to Wig" version="1.0.0">
+<tool id="BedToWig" name="Interval 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 f58706d4d421 -r 3e477c7e0e73 galaxy-conf/LogTransform.xml
--- a/galaxy-conf/LogTransform.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/LogTransform.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="Logger" name="Log transform" version="1.0.0">
+<tool id="WigLogTransform" name="Log transform" version="1.1.0">
   <description>a (Big)Wig file</description>
   <command interpreter="sh">galaxyToolRunner.sh wigmath.LogTransform -i $input -b $base -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/MapDyads.xml
--- a/galaxy-conf/MapDyads.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/MapDyads.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="MapDyads" name="Map dyads" version="1.0.0">
+<tool id="MapDyads" name="Map dyads" version="1.1.0">
   <description>from sequencing reads</description>
   <command interpreter="sh">
     galaxyToolRunner.sh nucleosomes.MapDyads -i $input -a ${chromInfo} -o $output
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/MovingAverageSmooth.xml
--- a/galaxy-conf/MovingAverageSmooth.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/MovingAverageSmooth.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="MovingAverageSmoother" name="Moving average smooth" version="1.0.0">
+<tool id="WigMovingAverage" name="Moving average smooth" version="1.1.0">
   <description>a (Big)Wig file</description>
   <command interpreter="sh">galaxyToolRunner.sh wigmath.MovingAverageSmooth -i $input -w $W -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Multiply.xml
--- a/galaxy-conf/Multiply.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/Multiply.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="WigMultiply" name="Multiply" version="1.0.0">
+<tool id="WigMultiply" name="Multiply" version="1.1.0">
   <description>(Big)Wig files</description>
   <command interpreter="sh">
     galaxyToolRunner.sh wigmath.Multiply -o $output
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/NRLCalculator.xml
--- a/galaxy-conf/NRLCalculator.xml	Sat May 19 10:40:16 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-<tool id="NRLCalculator" name="Compute the NRL" version="1.0.0">
-  <description>from nucleosome calls</description>
-  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.NRLCalculator -i $input -l $windows -o $output</command>
-  <inputs>
-      <param format="tabular" name="input" type="data" label="Nucleosome calls" />
-      <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals/genes" />
-  </inputs>
-  <outputs>
-      <data format="tabular" name="output" />
-  </outputs>
-  
-<help>
-  
-This tool calculates the distance between adjacent nucleosome calls (dyads) emanating from the 5' end of an interval. For each interval, the distance is calculated from the +1 to +2 nucleosome, +2 to +3 nucleosome, etc. These distances are appended as additional columns for each interval. ::
-
-  chr  start  stop  id  alignment  strand  +1-to-+2  +2-to-+3  ...
-  
-Each interval will have a different number of columns based on the number of nucleosome calls that were in that interval.
-  
------
-  
-.. class:: warningmark
-
-Because the distances are calculated from the 5' end of each gene, as you move into the gene body it becomes more likely that a nucleosome call will be skipped, resulting in an outlier distance (~320bp rather than ~165bp). In addition, nucleosome calls in fuzzy regions tend to be inaccurate, so the NRL distances will not be robust.
-  
-.. class:: warningmark
-
-This tool requires a set of nucleosome calls as input in the format created by the Nucleosomes -> Call Nucleosomes tool.
-
-.. class:: warningmark
-
-Intervals must be provided in Bed, BedGraph, or GFF format. BedGraph intervals are always considered to be on the + strand.
-
-</help>
-</tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/PercusDecomposition.xml
--- a/galaxy-conf/PercusDecomposition.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/PercusDecomposition.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="PercusDecomposition" name="Derive Percus energy landscape" version="1.0.0">
+<tool id="PercusDecomposition" name="Derive Percus energy landscape" version="1.1.0">
   <description>from occupancy data</description>
   <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PercusDecomposition -d $dyads -n $N -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/PredictFAIRESignal.xml
--- a/galaxy-conf/PredictFAIRESignal.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/PredictFAIRESignal.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,11 +1,11 @@
-<tool id="PredictFAIRE" name="Predict FAIRE signal" version="1.0.0">
+<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 (bp)" />
+      <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" />
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/RollingReadLength.xml
--- a/galaxy-conf/RollingReadLength.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/RollingReadLength.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="RollingReadLength" name="Compute mean fragment length" version="1.0.0">
+<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>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Scale.xml
--- a/galaxy-conf/Scale.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/Scale.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,9 +1,10 @@
-<tool id="WigScale" name="Scale" version="1.0.0">
+<tool id="WigScale" name="Scale" version="1.2.0">
   <description>a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.Scale -i $input -m $M -o $output</command>
+  <command interpreter="sh">galaxyToolRunner.sh wigmath.Scale -i $input -m $M $chr -o $output</command>
   <inputs>
     <param format="bigwig,wig" name="input" type="data" label="Scale the data in" />
     <param name="M" type="float" value="0" label="Multiply by (leave 0 to scale by 1/mean)" />
+    <param name="chr" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Scale chromosomes to 1/mean individually (no effect if scale factor is specified)" />
   </inputs>
   <outputs>
     <data format="wig" name="output" metadata_source="input" />
@@ -49,7 +50,7 @@
   
   <help>
 
-This tool will multiply all values in a Wig file by a scalar. For example, this can be used to normalize to read depth by multiplying by 1/(# reads). By default, the tool will scale to 1/(mean value), which is equivalent to dividing by coverage and multiplying by the size of the genome. The resulting output file should have mean 1.
+This tool will multiply all values in a Wig file by a scale factor. For example, this can be used to normalize to read depth by multiplying by 1/(# reads). By default, the tool will scale to 1/(mean value), which is equivalent to dividing by coverage and multiplying by the size of the genome. The resulting output file should have mean 1.
     
 .. class:: infomark
 
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Shift.xml
--- a/galaxy-conf/Shift.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/Shift.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,9 +1,10 @@
-<tool id="WigShift" name="Mean shift" version="1.0.0">
+<tool id="WigShift" name="Mean shift" version="1.2.0">
   <description>a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.Shift -i $input -m $M -o $output</command>
+  <command interpreter="sh">galaxyToolRunner.sh wigmath.Shift -i $input -m $M $chr -o $output</command>
   <inputs>
     <param format="bigwig,wig" name="input" type="data" label="Shift the data in" />
     <param name="M" type="float" value="0" label="To have mean" />
+    <param name="chr" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Mean-shift chromosomes individually" />
   </inputs>
   <outputs>
     <data format="wig" name="output" metadata_source="input" />
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/StripMatrix.xml
--- a/galaxy-conf/StripMatrix.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/StripMatrix.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="StripMatrix" name="Strip headers" version="1.0.0">
+<tool id="StripMatrix" name="Strip headers" version="1.1.0">
   <description>from an aligned matrix</description>
   <command interpreter="sh">galaxyToolRunner.sh visualization.StripMatrix -i $input -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Subtract.xml
--- a/galaxy-conf/Subtract.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/Subtract.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="WigSubtract" name="Subtract" version="1.0.0">
+<tool id="WigSubtract" name="Subtract" version="1.1.0">
   <description>two (Big)Wig files</description>
   <command interpreter="sh">galaxyToolRunner.sh wigmath.Subtract -m $minuend -s $subtrahend -o $output</command>
   <inputs>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Summary.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/Summary.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -0,0 +1,83 @@
+<tool id="WigSummary" name="Output a summary" version="1.1.0">
+  <description>of a (Big)Wig file</description>
+  <command interpreter="sh">galaxyToolRunner.sh wigmath.Summary -i $input -o $output</command>
+  <inputs>
+      <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" />
+  </inputs>
+  <outputs>
+      <data format="txt" name="output" />
+  </outputs>
+  <tests>
+      <test>
+      	<param name="input" value="wigmath1.wig"/>
+      	<output name="output" file="wigsummary1.txt"/>
+      </test>
+      <test>
+      	<param name="input" value="test.wig"/>
+      	<output name="output" file="wigsummary2.txt"/>
+      </test>
+      <test>
+      	<param name="input" value="test.bw"/>
+      	<output name="output" file="wigsummary3.txt"/>
+      </test>
+  </tests>
+  
+<help>
+  
+This tool will output a summary of a Wig or BigWig file, including information about the chromosomes and types of contigs in the Wig file, as well as basic descriptive statistics.
+
+-----
+
+**Example:**
+
+The following is an example of the output of this tool ::
+
+    ASCII Text Wiggle file: track type=wiggle_0
+    Chromosomes:
+      2micron start=1 stop=6318
+      chrVI start=1 stop=270148
+      chrI start=1 stop=230208
+      chrIII start=1 stop=316617
+      chrXII start=1 stop=1078175
+      chrXV start=1 stop=1091289
+      chrXVI start=1 stop=948062
+      chrII start=1 stop=813178
+      chrVIII start=1 stop=562643
+      chrX start=1 stop=745742
+      chrXIII start=1 stop=924429
+      chrV start=1 stop=576869
+      chrXIV start=1 stop=784333
+      chrIV start=1 stop=1531919
+      chrXI start=1 stop=666454
+      chrIX start=1 stop=439885
+      chrM start=1 stop=85779
+      chrVII start=1 stop=1090947
+    Contigs:
+      fixedStep chrom=2micron start=1 span=1 step=1
+      fixedStep chrom=chrVI start=1 span=1 step=1
+      fixedStep chrom=chrI start=1 span=1 step=1
+      fixedStep chrom=chrIII start=1 span=1 step=1
+      fixedStep chrom=chrXII start=1 span=1 step=1
+      fixedStep chrom=chrXVI start=1 span=1 step=1
+      fixedStep chrom=chrXV start=1 span=1 step=1
+      fixedStep chrom=chrII start=1 span=1 step=1
+      fixedStep chrom=chrVIII start=1 span=1 step=1
+      fixedStep chrom=chrXIII start=1 span=1 step=1
+      fixedStep chrom=chrX start=1 span=1 step=1
+      fixedStep chrom=chrV start=1 span=1 step=1
+      fixedStep chrom=chrXIV start=1 span=1 step=1
+      fixedStep chrom=chrIV start=1 span=1 step=1
+      fixedStep chrom=chrXI start=1 span=1 step=1
+      fixedStep chrom=chrIX start=1 span=1 step=1
+      fixedStep chrom=chrM start=1 span=1 step=1
+      fixedStep chrom=chrVII start=1 span=1 step=1
+    Basic Statistics:
+      Mean:               1.000000164913575
+      Standard Deviation: 1.8843731523620193
+      Total:              1.2162997005843896E7
+      Bases Covered:      12162995
+      Min value:          0.0
+      Max value:          277.98996
+  
+</help>
+</tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/ValueDistribution.xml
--- a/galaxy-conf/ValueDistribution.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/ValueDistribution.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="ValueDistribution" name="Compute the value distribution" version="1.0.0">
+<tool id="WigValueDistribution" name="Compute the value distribution" version="1.1.0">
   <description>of a (Big)Wig file</description>
   <command interpreter="sh">galaxyToolRunner.sh wigmath.ValueDistribution -i $input 
     #if str( $min ) != ''
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/WaveletTransform.xml
--- a/galaxy-conf/WaveletTransform.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/WaveletTransform.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -9,7 +9,7 @@
       <param name="stop" type="integer" value="1000" label="Stop base pair" />
       <param name="min" type="integer" value="10" label="Minimum wavelet size (bp)" />
       <param name="max" type="integer" value="400" label="Maximum wavelet size (bp)" />
-      <param name="N" type="integer" value="1" label="Step size (bp)" />
+      <param name="N" type="integer" value="1" label="Scaling step size (bp)" />
   </inputs>
   <outputs>
       <data format="tabular" name="output" />
@@ -17,5 +17,24 @@
   
 <help>
   
+This tool will perform a Wavelet_ scaling_ analysis on an interval of genomic data. For each base pair in the interval, the similarity (correlation) is calculated between the data and the wavelet over a range of scales. This can be used to identify high-frequency and low-frequency features in the data. The output is a matrix in matrix2png format that can be used to generate a heatmap: along the x-axis (columns) are the base pairs in the interval, along the y-axis (rows) are the correlation coefficients for each Wavelet size, with the largest Wavelet scale at the top and the smallest scale at the bottom.
+
+.. _Wavelet: http://en.wikipedia.org/wiki/Wavelet
+
+.. _scaling: http://en.wikipedia.org/wiki/Scaleogram
+
+-----
+
+**Syntax**
+
+- **Input data** is the genomic data on which to compute the Wavelet scaling analysis.
+- **Wavelet** a single column of values representing a discrete Wavelet.
+- **Chromosome** a locus in the genome
+- **Start base pair** a locus in the genome
+- **Stop base pair** a locus in the genome
+- **Minimum wavelet size** the smallest Wavelet to analyze
+- **Minimum wavelet size** the largest Wavelet to analyze
+- **Scaling step size** the step size for the range of wavelet scales. The provided wavelet will be scaled to each size in the set min:step:max by interpolating the provided wavelet.
+  
 </help>
 </tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/WigCorrelate.xml
--- a/galaxy-conf/WigCorrelate.xml	Sat May 19 10:40:16 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-<tool id="WigCorrelate" name="Correlate" version="1.0.0">
-  <description>multiple (Big)Wig files</description>
-  <command interpreter="sh">
-    galaxyToolRunner.sh wigmath.WigCorrelate -w $window -s $step -t $type -o $output
-      #for $input in $inputs
-        ${input.file}
-      #end for
-  </command>
-  <inputs>
-      <repeat name="inputs" title="(Big)Wig file">
-        <param name="file" type="data" format="bigwig,wig" />
-      </repeat>
-      <param name="window" type="integer" value="100" label="Window size (bp)" />
-      <param name="step" type="integer" value="50" label="Sliding step size (bp)" />
-      <param name="type" type="select" label="Correlation metric">
-      	<option value="pearson">Pearson</option>
-      	<option value="spearman">Spearman</option>
-      </param>
-  </inputs>
-  <outputs>
-      <data format="tabular" name="output" />
-  </outputs>
-  
-<help>
-  
-This tool will compute a correlation matrix between the supplied Wig or BigWig files. Each row/column in the matrix is added in the order that files are added above, starting from the top left. The Wig file is downsampled into sliding windows with the specified bin size and shift by computing the mean value in each window. These windows are then correlated using either Pearson_'s Product-Moment correlation coefficient or Spearman_'s rank correlation coefficient. If the window size is set to 1, the correlation is calculated between all base pairs in the genome.
-  
-.. _Pearson: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient
-
-.. _Spearman: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
-  
------
-
-**Syntax**
-
-- **Inputs** are the genomic data to correlate
-- **Window size** is the size of the window to bin data into
-- **Sliding step size** is the shift step size of the sliding window used during binning
-- **Correlation metric** is the type of correlation to calculate
-  
------
-
-.. class:: warningmark
-
-**WARN:** In order to calculate the correlation coefficient, the data is loaded into entirely into memory. For large genomes, this may require a lot of RAM unless comparably larger window sizes are used.
-
------
-
-**Citation**
-
-This tool was inspired by ACT_ from the Gerstein lab.
-
-.. _ACT: http://act.gersteinlab.org
-
-J Jee*, J Rozowsky*, KY Yip*, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein. ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks. (2011) Bioinformatics 27(8): 1152-4.
-  
-</help>
-</tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/WigSummary.xml
--- a/galaxy-conf/WigSummary.xml	Sat May 19 10:40:16 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-<tool id="WigStats" name="Output a summary" version="1.0.0">
-  <description>of a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.WigSummary -i $input -o $output</command>
-  <inputs>
-      <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" />
-  </inputs>
-  <outputs>
-      <data format="txt" name="output" />
-  </outputs>
-  <tests>
-      <test>
-      	<param name="input" value="wigmath1.wig"/>
-      	<output name="output" file="wigsummary1.txt"/>
-      </test>
-      <test>
-      	<param name="input" value="test.wig"/>
-      	<output name="output" file="wigsummary2.txt"/>
-      </test>
-      <test>
-      	<param name="input" value="test.bw"/>
-      	<output name="output" file="wigsummary3.txt"/>
-      </test>
-  </tests>
-  
-<help>
-  
-This tool will output a summary of a Wig or BigWig file, including information about the chromosomes and types of contigs in the Wig file, as well as basic descriptive statistics.
-
------
-
-**Example:**
-
-The following is an example of the output of this tool ::
-
-    ASCII Text Wiggle file: track type=wiggle_0
-    Chromosomes:
-      2micron start=1 stop=6318
-      chrVI start=1 stop=270148
-      chrI start=1 stop=230208
-      chrIII start=1 stop=316617
-      chrXII start=1 stop=1078175
-      chrXV start=1 stop=1091289
-      chrXVI start=1 stop=948062
-      chrII start=1 stop=813178
-      chrVIII start=1 stop=562643
-      chrX start=1 stop=745742
-      chrXIII start=1 stop=924429
-      chrV start=1 stop=576869
-      chrXIV start=1 stop=784333
-      chrIV start=1 stop=1531919
-      chrXI start=1 stop=666454
-      chrIX start=1 stop=439885
-      chrM start=1 stop=85779
-      chrVII start=1 stop=1090947
-    Contigs:
-      fixedStep chrom=2micron start=1 span=1 step=1
-      fixedStep chrom=chrVI start=1 span=1 step=1
-      fixedStep chrom=chrI start=1 span=1 step=1
-      fixedStep chrom=chrIII start=1 span=1 step=1
-      fixedStep chrom=chrXII start=1 span=1 step=1
-      fixedStep chrom=chrXVI start=1 span=1 step=1
-      fixedStep chrom=chrXV start=1 span=1 step=1
-      fixedStep chrom=chrII start=1 span=1 step=1
-      fixedStep chrom=chrVIII start=1 span=1 step=1
-      fixedStep chrom=chrXIII start=1 span=1 step=1
-      fixedStep chrom=chrX start=1 span=1 step=1
-      fixedStep chrom=chrV start=1 span=1 step=1
-      fixedStep chrom=chrXIV start=1 span=1 step=1
-      fixedStep chrom=chrIV start=1 span=1 step=1
-      fixedStep chrom=chrXI start=1 span=1 step=1
-      fixedStep chrom=chrIX start=1 span=1 step=1
-      fixedStep chrom=chrM start=1 span=1 step=1
-      fixedStep chrom=chrVII start=1 span=1 step=1
-    Basic Statistics:
-      Mean:               1.000000164913575
-      Standard Deviation: 1.8843731523620193
-      Total:              1.2162997005843896E7
-      Bases Covered:      12162995
-      Min value:          0.0
-      Max value:          277.98996
-  
-</help>
-</tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/ZScore.xml
--- a/galaxy-conf/ZScore.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/ZScore.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,8 +1,9 @@
-<tool id="WigZScore" name="Z-Score" version="1.0.0">
+<tool id="WigZScore" name="Z-Score" version="1.2.0">
   <description>a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.ZScore -i $input -o $output</command>
+  <command interpreter="sh">galaxyToolRunner.sh wigmath.ZScore -i $input $chr -o $output</command>
   <inputs>
       <param format="bigwig,wig" name="input" type="data" label="Z-score the data in" />
+      <param name="chr" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Z-score chromosomes individually" />
   </inputs>
   <outputs>
       <data format="wig" name="output" metadata_source="input" />
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/Zinba.xml
--- a/galaxy-conf/Zinba.xml	Sat May 19 10:40:16 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-<tool id="Zinba" name="Call peaks" version="1.0.0">
-  <description>with ZINBA</description>
-  <command interpreter="sh">runZINBA.sh -i $input -o $output</command>
-  <inputs>
-      <param format="bed" name="reads" type="data" label="Mapped reads (in BED format)" />
-      <param format="wig" name="basecount" type="data" label="Coverage track (base align counts)" />
-      
-  </inputs>
-  <outputs>
-      <data format="wig" name="output" metadata_source="input" />
-  </outputs>
-  <help>
-
-
-  </help>
-</tool>
diff -r f58706d4d421 -r 3e477c7e0e73 galaxy-conf/log4j.properties
--- a/galaxy-conf/log4j.properties	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/log4j.properties	Sat Jun 09 16:03:59 2012 -0400
@@ -7,4 +7,6 @@
 log4j.appender.stdout.layout.ConversionPattern=%m%n
 
 # Only output errors from the BigWig library
-log4j.logger.org.broad.igv.bbfile=ERROR
\ No newline at end of file
+log4j.logger.org.broad.igv.bbfile=ERROR
+# Only output errors from java-genomics-io
+log4j.logger.edu.unc.genomics.io=ERROR
\ No newline at end of file
diff -r f58706d4d421 -r 3e477c7e0e73 lib/java-genomics-io.jar
Binary file lib/java-genomics-io.jar has changed
diff -r f58706d4d421 -r 3e477c7e0e73 lib/jcommander-1.20.jar
Binary file lib/jcommander-1.20.jar has changed
diff -r f58706d4d421 -r 3e477c7e0e73 lib/jcommander-1.27.jar
Binary file lib/jcommander-1.27.jar has changed
diff -r f58706d4d421 -r 3e477c7e0e73 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sat May 19 10:40:16 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
-<tables>
-    <!-- Locations of all fasta files under genome directory -->
-    <table name="all_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc" />
-    </table>
-    <!-- Locations of indexes in the BFAST mapper format -->
-    <table name="bfast_indexes" comment_char="#">
-        <columns>value, dbkey, formats, name, path</columns>
-        <file path="tool-data/bfast_indexes.loc" />
-    </table>
-    <!-- Locations of nucleotide (mega)blast databases -->
-    <table name="blastdb" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb.loc" />
-    </table>
-    <!-- Locations of protein (mega)blast databases -->
-    <table name="blastdb_p" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb_p.loc" />
-    </table>
-    <!-- Locations of indexes in the Bowtie mapper format -->
-    <table name="bowtie_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices.loc" />
-    </table>
-    <!-- Locations of indexes in the Bowtie2 mapper format -->
-    <table name="bowtie2_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie2_indices.loc" />
-    </table>
-    <!-- Locations of indexes in the Bowtie color-space mapper format -->
-    <table name="bowtie_indexes_color" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices_color.loc" />
-    </table>
-    <!-- Locations of indexes in the BWA mapper format -->
-    <table name="bwa_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bwa_index.loc" />
-    </table>
-    <!-- Locations of indexes in the BWA color-space mapper format -->
-    <table name="bwa_indexes_color" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bwa_index_color.loc" />
-    </table>
-    <!-- Locations of MAF files that have been indexed with bx-python -->
-    <table name="indexed_maf_files">
-        <columns>name, value, dbkey, species</columns>
-        <file path="tool-data/maf_index.loc" />
-    </table>
-    <!-- Locations of fasta files appropriate for NGS simulation -->
-    <table name="ngs_sim_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/ngs_sim_fasta.loc" />
-    </table>
-    <!-- Locations of 2bit sequence files for use in Lastz -->
-    <table name="lastz_seqs" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/lastz_seqs.loc" />
-    </table>
-    <!-- Locations of PerM base index files -->
-    <table name="perm_base_indexes" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/perm_base_index.loc" />
-    </table>
-    <!-- Locations of PerM color-space index files -->
-    <table name="perm_color_indexes" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/perm_color_index.loc" />
-    </table>
-    <!-- Location of SAMTools indexes and other files -->
-    <table name="sam_fa_indexes" comment_char="#">
-        <columns>line_type, value, path</columns>
-        <file path="tool-data/sam_fa_indices.loc" />
-    </table>
-    <!-- Location of Picard dict file and other files -->
-    <table name="picard_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.loc" />
-    </table>
-    <!-- Location of Picard dict files valid for GATK -->
-    <table name="gatk_picard_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/gatk_sorted_picard_index.loc" />
-    </table>
-    <!-- Available of GATK references -->
-    <table name="gatk_annotations" comment_char="#">
-        <columns>value, name, gatk_value, tools_valid_for</columns>
-        <file path="tool-data/gatk_annotations.txt" />
-    </table>
-    <!-- Location of SRMA dict file and other files -->
-    <table name="srma_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.loc" />
-    </table>
-    <!-- Locations of indexes in the Bowtie mapper format for TopHat to use -->
-    <table name="tophat_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices.loc" />
-    </table>
-    <!-- Locations of indexes in the Bowtie color-space mapper format for TopHat to use -->
-    <table name="tophat_indexes_color" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices_color.loc" />
-    </table>
-    <!-- Locations of configurations in the CCAT peak/region caller format -->
-    <table name="ccat_configurations" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/ccat_configurations.loc" />
-    </table>
-    <!-- Location of Mosaik files -->
-    <table name="mosaik_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/mosaik_index.loc" />
-    </table>
-</tables>