Mercurial > repos > timpalpant > java_genomics_toolkit

changeset 5:604c98e58034

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Uploaded
author timpalpant
date Tue, 14 Feb 2012 13:04:54 -0500
parents 4b32ed5d4a1b
children 422ac2bbb274
files dist/java-genomics-toolkit.jar galaxy-conf/._BaseAlignCounts.xml galaxy-conf/BaseAlignCounts.xml galaxy-conf/MapDyads.xml galaxy-conf/NRLCalculator.xml galaxy-conf/Phasogram.xml
diffstat 6 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
Binary file dist/java-genomics-toolkit.jar has changed
Binary file galaxy-conf/._BaseAlignCounts.xml has changed
--- 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)" />
--- 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
--- 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" />
--- 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)" />