# HG changeset patch
# User timpalpant
# Date 1329242694 18000
# Node ID 604c98e58034fffdd956ead962427dbfa3508503
# Parent  4b32ed5d4a1b9a2d1df23fd327e0ed3e78eda22c
Uploaded

diff -r 4b32ed5d4a1b -r 604c98e58034 dist/java-genomics-toolkit.jar
Binary file dist/java-genomics-toolkit.jar has changed
diff -r 4b32ed5d4a1b -r 604c98e58034 galaxy-conf/._BaseAlignCounts.xml
Binary file galaxy-conf/._BaseAlignCounts.xml has changed
diff -r 4b32ed5d4a1b -r 604c98e58034 galaxy-conf/BaseAlignCounts.xml
--- a/galaxy-conf/BaseAlignCounts.xml	Tue Feb 14 00:59:33 2012 -0500
+++ b/galaxy-conf/BaseAlignCounts.xml	Tue Feb 14 13:04:54 2012 -0500
@@ -1,6 +1,6 @@
 <tool id="BaseAlignCounts" name="Map coverage" version="1.0.0">
   <description>of sequencing reads</description>
-  <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -g ${chromInfo} -x $X -o $output</command>
+  <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
   <inputs>
     <param name="input" type="data" format="bam,sam,bed,bedgraph" label="Sequencing reads" />
     <param name="X" type="integer" value="0" label="In silico extension (leave 0 for read length)" />
diff -r 4b32ed5d4a1b -r 604c98e58034 galaxy-conf/MapDyads.xml
--- a/galaxy-conf/MapDyads.xml	Tue Feb 14 00:59:33 2012 -0500
+++ b/galaxy-conf/MapDyads.xml	Tue Feb 14 13:04:54 2012 -0500
@@ -1,7 +1,7 @@
 <tool id="MapDyads" name="Map dyads" version="1.0.0">
   <description>from sequencing reads</description>
   <command interpreter="sh">
-    galaxyToolRunner.sh nucleosome.MapDyads -i $input -a ${chromInfo} -o $output
+    galaxyToolRunner.sh nucleosomes.MapDyads -i $input -a ${chromInfo} -o $output
     #if $type.read == 'single'
       -s $type.size
     #end if
diff -r 4b32ed5d4a1b -r 604c98e58034 galaxy-conf/NRLCalculator.xml
--- a/galaxy-conf/NRLCalculator.xml	Tue Feb 14 00:59:33 2012 -0500
+++ b/galaxy-conf/NRLCalculator.xml	Tue Feb 14 13:04:54 2012 -0500
@@ -1,6 +1,6 @@
 <tool id="NRLCalculator" name="Compute the NRL" version="1.0.0">
   <description>from nucleosome calls</description>
-  <command interpreter="sh">galaxyToolRunner.sh nucleosome.NRLCalculator -i $input -l $windows -o $output</command>
+  <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" />
diff -r 4b32ed5d4a1b -r 604c98e58034 galaxy-conf/Phasogram.xml
--- a/galaxy-conf/Phasogram.xml	Tue Feb 14 00:59:33 2012 -0500
+++ b/galaxy-conf/Phasogram.xml	Tue Feb 14 13:04:54 2012 -0500
@@ -1,6 +1,6 @@
 <tool id="Phasogram" name="Make phasogram" version="1.0.0">
   <description>of dyads</description>
-  <command interpreter="ruby">phasogram.rb -i $input -m $max -o $output</command>
+  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.Phasogram -i $input -m $max -o $output</command>
   <inputs>
     <param name="input" type="data" format="bigwig,wig" label="Dyads BigWig file" />
     <param name="max" type="integer" value="1000" label="Maximum phase shift (bp)" />