# HG changeset patch
# User mzytnicki
# Date 1366990669 14400
# Node ID 938a8ead56b869853cb8e690e5b852c3c9e07ec8
# Parent  6b9afa2bdda39eadc427a7487eeebef8ec0dd3c5
Uploaded

diff -r 6b9afa2bdda3 -r 938a8ead56b8 tool_conf.xml
--- a/tool_conf.xml	Fri Apr 26 05:54:37 2013 -0400
+++ b/tool_conf.xml	Fri Apr 26 11:37:49 2013 -0400
@@ -1,48 +1,48 @@
   <section id="s_mart" name="S-MART" version="">
-    <label id="Comparison" text="Comparison Tools" version="">
-      <tool id="s_martXML/CompareOverlappingSmallQuery.xml"/>
-      <tool id="s_martXML/CompareOverlappingSmallRef.xml"/>
-      <tool id="s_martXML/CompareOverlapping.xml"/>
-      <tool id="s_martXML/getDifference.xml"/>
-      <tool id="s_martXML/ComputeCoverage.xml"/>
-      <tool id="s_martXML/GetFlanking.xml"/>
-      <tool id="s_martXML/GetDifferentialExpression.xml"/>
-    <label id="Merge" text="Merge Tools" version="">
-      <tool id="s_martXML/MergingDataClusterize.xml"/>
-      <tool id="s_martXML/mergeTranscriptLists.xml"/>
-      <tool id="s_martXML/collapseReads.xml"/>
-      <tool id="s_martXML/clusterizeBySlidingWindows.xml"/>
-      <tool id="s_martXML/mergeSlidingWindowsClusters.xml"/>
-    <label id="Visualization" text="Visualization Tools" version="">
-      <tool id="s_martXML/getDistribution.xml"/>
-      <tool id="s_martXML/GetDistance.xml"/>
-      <tool id="s_martXML/GetSizes.xml"/>
-      <tool id="s_martXML/plotCoverage.xml"/>
-      <tool id="s_martXML/getLetterDistribution1.xml"/>
-      <tool id="s_martXML/plotTranscriptList.xml"/>
-    <label id="Sequence" text="Sequence Tools" version="">
-      <tool id="s_martXML/CountReadGCPercent.xml"/>
-    <label id="Modification" text="Modification Tools" version="">
-      <tool id="s_martXML/modifyGenomicCoordinates.xml"/>
-      <tool id="s_martXML/modifySequenceList.xml"/>
-      <tool id="s_martXML/trimSequences.xml"/>
-    <label id="Selection" text="Selection Tools" version="">
-      <tool id="s_martXML/getExons.xml"/>
-      <tool id="s_martXML/getIntrons.xml"/>
-      <tool id="s_martXML/restrictFromSize.xml"/>
-      <tool id="s_martXML/restrictTranscriptList.xml"/>
-    <label id="Conversion" text="Conversion Tools" version="">
-      <tool id="s_martXML/ConvertTranscriptFile.xml"/>
-      <tool id="s_martXML/coordinatesToSequence.xml"/>
-      <tool id="s_martXML/mapperAnalyzer.xml"/>
-    <label id="WIG" text="WIG Manipulation Tools" version="">
-      <tool id="s_martXML/getWigData.xml"/>
-      <tool id="s_martXML/getWigDistance.xml"/>
-      <tool id="s_martXML/getWigProfile.xml"/>
-    <label id="GFF" text="GFF Manipulation Tools" version="">
-      <tool id="s_martXML/CleanTranscriptFile.xml"/>
-      <tool id="s_martXML/changeTagName.xml"/>
-      <tool id="s_martXML/changeGffFeatures.xml"/>
-      <tool id="s_martXML/removeExonLines.xml"/>
-      <tool id="s_martXML/SelectByTag.xml"/>
+    <label id="Smart_Comparison" text="Comparison Tools" version="">
+      <tool file="s_mart/CompareOverlappingSmallQuery.xml"/>
+      <tool file="s_mart/CompareOverlappingSmallRef.xml"/>
+      <tool file="s_mart/compareOverlapping.xml"/>
+      <tool file="s_mart/getDifference.xml"/>
+      <tool file="s_mart/computeCoverage.xml"/>
+      <tool file="s_mart/GetFlanking.xml"/>
+      <tool file="s_mart/GetDifferentialExpression.xml"/>
+    <label id="Smart_Merge" text="Merge Tools" version="">
+      <tool file="s_mart/clusterize.xml"/>
+      <tool file="s_mart/mergeTranscriptLists.xml"/>
+      <tool file="s_mart/CollapseReads.xml"/>
+      <tool file="s_mart/clusterizeBySlidingWindows.xml"/>
+      <tool file="s_mart/mergeSlidingWindowsClusters.xml"/>
+    <label id="Smart_Visualization" text="Visualization Tools" version="">
+      <tool file="s_mart/getDistribution.xml"/>
+      <tool file="s_mart/getDistance.xml"/>
+      <tool file="s_mart/getSizes.xml"/>
+      <tool file="s_mart/plotCoverage.xml"/>
+      <tool file="s_mart/WrappGetLetterDistribution1.xml"/>
+      <tool file="s_mart/plotTranscriptList.xml"/>
+    <label id="Smart_Sequence" text="Sequence Tools" version="">
+      <tool file="s_mart/CountReadGCPercent.xml"/>
+    <label id="Smart_Modification" text="Modification Tools" version="">
+      <tool file="s_mart/modifyGenomicCoordinates.xml"/>
+      <tool file="s_mart/modifySequenceList.xml"/>
+      <tool file="s_mart/trimSequences.xml"/>
+    <label id="Smart_Selection" text="Selection Tools" version="">
+      <tool file="s_mart/getExons.xml"/>
+      <tool file="s_mart/getIntrons.xml"/>
+      <tool file="s_mart/restrictFromSize.xml"/>
+      <tool file="s_mart/restrictTranscriptList.xml"/>
+    <label id="Smart_Conversion" text="Conversion Tools" version="">
+      <tool file="s_mart/ConvertTranscriptFile.xml"/>
+      <tool file="s_mart/coordinatesToSequence.xml"/>
+      <tool file="s_mart/mapperAnalyzer.xml"/>
+    <label id="Smart_WIG" text="WIG Manipulation Tools" version="">
+      <tool file="s_mart/getWigData.xml"/>
+      <tool file="s_mart/getWigDistance.xml"/>
+      <tool file="s_mart/getWigProfile.xml"/>
+    <label id="Smart_GFF" text="GFF Manipulation Tools" version="">
+      <tool file="s_mart/CleanTranscriptFile.xml"/>
+      <tool file="s_mart/changeTagName.xml"/>
+      <tool file="s_mart/changeGffFeatures.xml"/>
+      <tool file="s_mart/removeExonLines.xml"/>
+      <tool file="s_mart/SelectByTag.xml"/>
   </section>