# HG changeset patch
# User timpalpant
# Date 1340158163 14400
# Node ID 727fbba02ef718fbc1c5102e6cf8f40cc893d52d
# Parent  51b28ce6ef7eb77795c56582ab764874407dad3b
Fix a bug in GeneTrackToWig where +/- strands were not merged correctly. Add option to vary the chunk size of tools that process chromosomes in chunks.

diff -r 51b28ce6ef7e -r 727fbba02ef7 dist/java-genomics-toolkit.jar
Binary file dist/java-genomics-toolkit.jar has changed
diff -r 51b28ce6ef7e -r 727fbba02ef7 galaxy-conf/._IntervalStats.xml
Binary file galaxy-conf/._IntervalStats.xml has changed
diff -r 51b28ce6ef7e -r 727fbba02ef7 galaxy-conf/IntervalStats.xml
--- a/galaxy-conf/IntervalStats.xml	Mon Jun 18 14:50:31 2012 -0400
+++ b/galaxy-conf/IntervalStats.xml	Tue Jun 19 22:09:23 2012 -0400
@@ -1,5 +1,5 @@
 <tool id="IntervalStats" name="Compute mean/min/max of intervals" version="1.0.0">
-  <description>of data in a Wiggle file</description>
+  <description>of data in a (Big)Wig file</description>
   <command interpreter="sh">
     galaxyToolRunner.sh ngs.IntervalStats -l $windows -s $stat -o $output
       #for $input in $inputs
@@ -7,7 +7,7 @@
       #end for
   </command>
   <inputs>
-      <repeat name="inputs" title="BigWig file">
+      <repeat name="inputs" title="(Big)Wig file">
         <param name="file" type="data" format="bigwig,wig" />
       </repeat>
       <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
diff -r 51b28ce6ef7e -r 727fbba02ef7 galaxy-conf/Scale.xml
--- a/galaxy-conf/Scale.xml	Mon Jun 18 14:50:31 2012 -0400
+++ b/galaxy-conf/Scale.xml	Tue Jun 19 22:09:23 2012 -0400
@@ -4,7 +4,7 @@
   <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)" />
+    <param name="chr" type="boolean" checked="false" truevalue="--bychr" 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" />
diff -r 51b28ce6ef7e -r 727fbba02ef7 galaxy-conf/Shift.xml
--- a/galaxy-conf/Shift.xml	Mon Jun 18 14:50:31 2012 -0400
+++ b/galaxy-conf/Shift.xml	Tue Jun 19 22:09:23 2012 -0400
@@ -4,7 +4,7 @@
   <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" />
+    <param name="chr" type="boolean" checked="false" truevalue="--bychr" falsevalue="" label="Mean-shift chromosomes individually" />
   </inputs>
   <outputs>
     <data format="wig" name="output" metadata_source="input" />
diff -r 51b28ce6ef7e -r 727fbba02ef7 galaxy-conf/ZScore.xml
--- a/galaxy-conf/ZScore.xml	Mon Jun 18 14:50:31 2012 -0400
+++ b/galaxy-conf/ZScore.xml	Tue Jun 19 22:09:23 2012 -0400
@@ -3,7 +3,7 @@
   <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" />
+      <param name="chr" type="boolean" checked="false" truevalue="--bychr" falsevalue="" label="Z-score chromosomes individually" />
   </inputs>
   <outputs>
       <data format="wig" name="output" metadata_source="input" />