# HG changeset patch
# User timpalpant
# Date 1333986623 14400
# Node ID b1952a90d4bffd6d819dd067ab21ec6d961ce90d
# Parent d063d22f4e80b381212233079dbb33220839ff50
Uploaded
diff -r d063d22f4e80 -r b1952a90d4bf dist/java-genomics-toolkit.jar
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._Add.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._Autocorrelation.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._Average.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._BaseAlignCounts.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._Divide.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._FilterOutlierRegions.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._FindAbsoluteMaxima.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._FindBoundaryNucleosomes.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._GaussianSmooth.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._GeneTrackToBedGraph.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._GeneTrackToWig.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._GreedyCaller.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._IntervalAverager.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._IntervalLengthDistribution.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._IntervalStats.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._IntervalToWig.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._KMeans.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._LogTransform.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._MapDyads.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._MatrixAligner.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._MovingAverageSmooth.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._Multiply.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._NRLCalculator.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._PercusDecomposition.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._PowerSpectrum.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._RollingReadLength.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._RomanNumeralize.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._Scale.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._StripMatrix.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._Subtract.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._ValueDistribution.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._WigSummary.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._ZScore.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._galaxyToolRunner.sh
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._log4j.properties
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/._matrix2png.xml
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diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/Average.xml
--- a/galaxy-conf/Average.xml Sat Mar 17 08:11:55 2012 -0400
+++ b/galaxy-conf/Average.xml Mon Apr 09 11:50:23 2012 -0400
@@ -7,8 +7,8 @@
#end for
-
-
+
+
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/Divide.xml
--- a/galaxy-conf/Divide.xml Sat Mar 17 08:11:55 2012 -0400
+++ b/galaxy-conf/Divide.xml Mon Apr 09 11:50:23 2012 -0400
@@ -36,8 +36,5 @@
- .. class:: warningmark
-
- This tool was contributed by Timothy Palpant.
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/FilterOutlierRegions.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/FilterOutlierRegions.xml Mon Apr 09 11:50:23 2012 -0400
@@ -0,0 +1,12 @@
+
+ in a (Big)Wig file
+ galaxyToolRunner.sh wigmath.FilterOutlierRegions -i $input -w $window -t $threshold -o $output
+
+
+
+
+
+
+
+
+
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/FindBoundaryNucleosomes.xml
--- a/galaxy-conf/FindBoundaryNucleosomes.xml Sat Mar 17 08:11:55 2012 -0400
+++ b/galaxy-conf/FindBoundaryNucleosomes.xml Mon Apr 09 11:50:23 2012 -0400
@@ -12,6 +12,6 @@
.. class:: warningmark
- Use the Greedy Caller tool to create a file of called nucleosomes, then use this tool to identify the first nucleosome's dyad position from the 5' or 3' end.
+ Use the Call Nucleosomes tool to create a file of called nucleosomes, then use this tool to identify the first nucleosome's dyad position from the 5' or 3' end.
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/GeneTrackToBedGraph.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/GeneTrackToBedGraph.xml Mon Apr 09 11:50:23 2012 -0400
@@ -0,0 +1,21 @@
+
+ converter
+ galaxyToolRunner.sh converters.GeneTrackToBedGraph -i $input -o $output
+
+
+
+
+
+
+
+
+
+.. class:: warningmark
+
+This tool will sum the counts from the forward and reverse strands in a GeneTrack index to create a BedGraph file.
+
+.. class:: warningmark
+
+This tool requires GeneTrack formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.
+
+
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/GeneTrackToWig.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/GeneTrackToWig.xml Mon Apr 09 11:50:23 2012 -0400
@@ -0,0 +1,18 @@
+
+ converter
+ galaxyToolRunner.sh converters.GeneTrackToWig -i $input $zero -a ${chromInfo} -o $output
+
+
+
+
+
+
+
+
+
+
+.. class:: warningmark
+
+This tool requires GeneTrack formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.
+
+
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/GreedyCaller.xml
--- a/galaxy-conf/GreedyCaller.xml Sat Mar 17 08:11:55 2012 -0400
+++ b/galaxy-conf/GreedyCaller.xml Mon Apr 09 11:50:23 2012 -0400
@@ -14,9 +14,5 @@
.. class:: warningmark
This tool requires dyad counts and smoothed dyad counts.
-
-.. class:: warningmark
-
-This tool was contributed by Timothy Palpant.
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/IntervalToWig.xml
--- a/galaxy-conf/IntervalToWig.xml Sat Mar 17 08:11:55 2012 -0400
+++ b/galaxy-conf/IntervalToWig.xml Mon Apr 09 11:50:23 2012 -0400
@@ -1,8 +1,9 @@
converter
- galaxyToolRunner.sh converters.IntervalToWig -i $input -a ${chromInfo} -o $output
+ galaxyToolRunner.sh converters.IntervalToWig -i $input $zero -a ${chromInfo} -o $output
+
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/KMeans.xml
--- a/galaxy-conf/KMeans.xml Sat Mar 17 08:11:55 2012 -0400
+++ b/galaxy-conf/KMeans.xml Mon Apr 09 11:50:23 2012 -0400
@@ -5,7 +5,7 @@
-
+
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/MapDyads.xml
--- a/galaxy-conf/MapDyads.xml Sat Mar 17 08:11:55 2012 -0400
+++ b/galaxy-conf/MapDyads.xml Mon Apr 09 11:50:23 2012 -0400
@@ -32,6 +32,6 @@
.. class:: warningmark
-For paired-end MNase data, read centers are approximated by using the center of the read. For single-end data, the estimated mononucleosome fragment length must be specified, which will be used to offset reads from the + and - strands.
+For paired-end MNase data, read centers are approximated using the center of the read. For single-end data, the estimated mononucleosome fragment length must be specified, which will be used to offset reads from the + and - strands.
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/PercusDecomposition.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/PercusDecomposition.xml Mon Apr 09 11:50:23 2012 -0400
@@ -0,0 +1,17 @@
+
+ from occupancy data
+ galaxyToolRunner.sh nucleosomes.PercusDecomposition -d $dyads -n $N -o $output
+
+
+
+
+
+
+
+
+
+.. class:: warningmark
+
+See Locke G, Tolkunov D, Moqtaderi Z, Struhl K and Morozov AV (2010) High-throughput sequencing reveals a simple model of nucleosome energetics. Proceedings of the National Academy of Sciences 107: 20998–21003 and Percus JK (1976) Equilibrium state of a classical fluid of hard rods in an external field. J Stat Phys 15: 505–511 for derivation.
+
+
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/RollingReadLength.xml
--- a/galaxy-conf/RollingReadLength.xml Sat Mar 17 08:11:55 2012 -0400
+++ b/galaxy-conf/RollingReadLength.xml Mon Apr 09 11:50:23 2012 -0400
@@ -12,9 +12,5 @@
.. class:: warningmark
This tool requires paired-end SAM, BAM, or Bed formatted data. Using single-end data will result in a constant read length.
-
-.. class:: warningmark
-
-This tool was contributed by Timothy Palpant.
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/ValueDistribution.xml
--- a/galaxy-conf/ValueDistribution.xml Sat Mar 17 08:11:55 2012 -0400
+++ b/galaxy-conf/ValueDistribution.xml Mon Apr 09 11:50:23 2012 -0400
@@ -1,8 +1,10 @@
of a (Big)Wig file
- galaxyToolRunner.sh wigmath.ValueDistribution -i $input -n $bins -o $output
+ galaxyToolRunner.sh wigmath.ValueDistribution -i $input --max $max --min $min -n $bins -o $output
+
+
diff -r d063d22f4e80 -r b1952a90d4bf galaxy-conf/matrix2png.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/matrix2png.xml Mon Apr 09 11:50:23 2012 -0400
@@ -0,0 +1,110 @@
+
+ using matrix2png
+ matrix2png
+ matrix2png -data $input
+ #if str( $range ) != ''
+ -range $range
+ #end if
+
+ -con $con
+ -size $size
+ -numcolors $numcolors
+ -minsize $minsize
+ -mincolor $mincolor
+ -maxcolor $maxcolor
+ -bkgcolor $bkgcolor
+ -missingcolor $missingcolor
+
+ #if str( $map ) != ''
+ -map $map
+ #end if
+
+ #if str( $discrete_color_maps.discrete ) != 'false'
+ -discrete
+ -dmap $dmap
+ #end if
+
+ #if str( $numr ) != ''
+ -numr $numr
+ #end if
+
+ #if str( $numc ) != ''
+ -numc $numc
+ #end if
+
+ -startrow $startrow
+ -startcol $startcol
+
+ #if str( $trim ) != '0'
+ -trim $trim
+ #end if
+
+ #if str( $title ) != ''
+ -title '$title'
+ #end if
+
+ $z $b $d $s $r $c $f $e $l $u
+
+ > $output
+
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+ .. class:: warningmark
+
+ This tool requires that matrix2png be available in Galaxy's PATH.
+
+ .. class:: warningmark
+
+ This tool requires tabular data with column AND row headers. For more information about the required format and usage instructions, see http://bioinformatics.ubc.ca/matrix2png/dataformat.html
+
+ .. class:: warningmark
+
+ It is recommended to specify the colorspace range.
+
+
diff -r d063d22f4e80 -r b1952a90d4bf lib/java-genomics-io.jar
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