# HG changeset patch
# User matces
# Date 1307477320 14400
# Node ID c28dd9f8ff89e5b2a5f0dd2b98edd6c5965109a6
# Parent  a21f481fbac232e664b6401cb0345cf4c82e09b8
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/.DS_Store
Binary file carpet-src-1/.DS_Store has changed
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/static/example_file/._CARPET_userManual.zip
Binary file carpet-src-1/static/example_file/._CARPET_userManual.zip has changed
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/static/example_file/._Expression_analysis_files.zip
Binary file carpet-src-1/static/example_file/._Expression_analysis_files.zip has changed
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/static/example_file/._GFF_file_norm.txt.zip
Binary file carpet-src-1/static/example_file/._GFF_file_norm.txt.zip has changed
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/static/example_file/._Pair_file.txt.zip
Binary file carpet-src-1/static/example_file/._Pair_file.txt.zip has changed
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/static/example_file/._UCSC_hs_refGene_chr19.zip
Binary file carpet-src-1/static/example_file/._UCSC_hs_refGene_chr19.zip has changed
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/static/example_file/._all_pair.txt.zip
Binary file carpet-src-1/static/example_file/._all_pair.txt.zip has changed
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/static/example_file/._log2ratio_file.txt.zip
Binary file carpet-src-1/static/example_file/._log2ratio_file.txt.zip has changed
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/static/example_file/._raw_value.txt.zip
Binary file carpet-src-1/static/example_file/._raw_value.txt.zip has changed
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/suite_config.xml
--- a/carpet-src-1/suite_config.xml	Tue Jun 07 16:05:13 2011 -0400
+++ b/carpet-src-1/suite_config.xml	Tue Jun 07 16:08:40 2011 -0400
@@ -1,4 +1,4 @@
-<suite id="CARPET_toolsuite" name="CARPET" version="1.0.0">
+<suite id="CARPET_toolsuite" name="CARPET" version="1.0.1">
         <description>This suite contains all tha CARPET tools created for Galaxy</description>
         <tool id="view_chip" name="ChipView" version="1.0.0">
              <description>looking into the chip</description>
@@ -15,7 +15,7 @@
         <tool id="common unique" name="Com&amp;Uni" version="1.1.0">
             <description>easy way to compare results</description>
         </tool>
-        <tool id="Annotation_RefSeq" name="GIN" version="1.2.0">
+        <tool id="Annotation_RefSeq" name="GIN" version="1.3.0">
             <description>Gene Intervals Notator</description>
         </tool>
         <tool id="Annotation visualization" name="GIN visualizator" version="1.0.0">
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/tools/.DS_Store
Binary file carpet-src-1/tools/.DS_Store has changed
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/tools/CARPET/MapToExon_RefSeqMat.xml
--- a/carpet-src-1/tools/CARPET/MapToExon_RefSeqMat.xml	Tue Jun 07 16:05:13 2011 -0400
+++ b/carpet-src-1/tools/CARPET/MapToExon_RefSeqMat.xml	Tue Jun 07 16:08:40 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="Annotation_RefSeq" name="GIN" version="1.2.0">
+<tool id="Annotation_RefSeq" name="GIN" version="1.3.0">
   <description>Gene Intervals Notator</description>
   <command interpreter="perl">MapToExon_RefSeqMat_new.pl $input1 $input2 $promoter $3prime $priority $output</command>
   <inputs>
diff -r a21f481fbac2 -r c28dd9f8ff89 carpet-src-1/tools/CARPET/MapToExon_RefSeqMat_new.pl
--- a/carpet-src-1/tools/CARPET/MapToExon_RefSeqMat_new.pl	Tue Jun 07 16:05:13 2011 -0400
+++ b/carpet-src-1/tools/CARPET/MapToExon_RefSeqMat_new.pl	Tue Jun 07 16:08:40 2011 -0400
@@ -144,7 +144,7 @@
 		}
 		$geneName=$kEle[$zname];
 		$exonStartref=$kEle[$zexonstart];
-		my $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand";
+		#my $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand";
 		
 		my @exonStart=split(",", $exonStartref);