From c7e6181c201c6e94cf7b4cd5d86931a227a1c338 Mon Sep 17 00:00:00 2001
From: Dave Bouvier <dave@bx.psu.edu>
Date: Mon, 14 Apr 2014 09:32:41 -0400
Subject: [PATCH] Fix issues with tool migration stage 10.

---
 scripts/migrate_tools/0010_tools.xml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/scripts/migrate_tools/0010_tools.xml b/scripts/migrate_tools/0010_tools.xml
index 1ead6aceb24..222e0ec6ce1 100644
--- a/scripts/migrate_tools/0010_tools.xml
+++ b/scripts/migrate_tools/0010_tools.xml
@@ -3,13 +3,13 @@
     <repository owner="devteam" name="analyze_covariates" changeset_revision="738bc749f9a3" description="Analyze Covariates">
         <tool id="gatk_analyze_covariates" version="0.0.5" file="gatk/analyze_covariates.xml" />
     </repository>
-    <repository owner="devteam" name="basecoverage" changeset_revision="642849141ae9" description="Base Coverage of all intervals">
+    <repository owner="devteam" name="basecoverage" changeset_revision="b8a9e718caa3" description="Base Coverage of all intervals">
         <tool id="gops_basecoverage_1" version="1.0.0" file="new_operations/basecoverage.xml" />
     </repository>
     <repository owner="devteam" name="best_regression_subsets" changeset_revision="4f33ec73e445" description="Perform Best-subsets Regression">
         <tool id="BestSubsetsRegression1" version="1.0.0" file="regVariation/best_regression_subsets.xml" />
     </repository>
-    <repository owner="devteam" name="cluster" changeset_revision="9fcc3a1c3d26" description="Cluster">
+    <repository owner="devteam" name="cluster" changeset_revision="520de69b107a" description="Cluster">
         <tool id="gops_cluster_1" version="1.0.0" file="new_operations/cluster.xml" />
     </repository>
     <repository owner="devteam" name="complement" changeset_revision="67c4ed724bfd" description="Complement intervals of a dataset">
@@ -18,7 +18,7 @@
     <repository owner="devteam" name="compute_q_values" changeset_revision="63abfc350814" description="Compute q-values based on multiple simultaneous tests p-values">
         <tool id="compute_q_values" version="1.0.1" file="regVariation/compute_q_values.xml" />
     </repository>
-    <repository owner="devteam" name="concat" changeset_revision="8aa939ace6ba" description="Concatenate two datasets into one dataset">
+    <repository owner="devteam" name="concat" changeset_revision="855580142a12" description="Concatenate two datasets into one dataset">
         <tool id="gops_concat_1" version="1.0.1" file="new_operations/concat.xml" />
     </repository>
     <repository owner="devteam" name="count_covariates" changeset_revision="14e304b70425" description="Count Covariates on BAM files">
@@ -36,7 +36,7 @@
     <repository owner="devteam" name="flanking_features" changeset_revision="90100b587723" description="Fetch closest non-overlapping feature for every interval">
         <tool id="flanking_features_1" version="4.0.1" file="new_operations/flanking_features.xml" />
     </repository>
-    <repository owner="devteam" name="get_flanks" changeset_revision="c3b1781c6fd1" description="Get flanks - returns flanking region/s for every gene">
+    <repository owner="devteam" name="get_flanks" changeset_revision="4b14d0e3a837" description="Get flanks - returns flanking region/s for every gene">
         <tool id="get_flanks1" version="1.0.0" file="new_operations/get_flanks.xml" />
     </repository>
     <repository owner="devteam" name="getindelrates_3way" changeset_revision="d427e5acb9ee" description="Estimate Indel Rates for 3-way alignments">
@@ -48,10 +48,10 @@
     <repository owner="devteam" name="indel_realigner" changeset_revision="bb0beda6cf83" description="Indel Realigner - perform local realignment">
         <tool id="gatk_indel_realigner" version="0.0.6" file="gatk/indel_realigner.xml" />
     </repository>
-    <repository owner="devteam" name="intersect" changeset_revision="81ad85f731b9" description="Intersect the intervals of two datasets">
+    <repository owner="devteam" name="intersect" changeset_revision="77641d5731c8" description="Intersect the intervals of two datasets">
         <tool id="gops_intersect_1" version="1.0.0" file="new_operations/intersect.xml" />
     </repository>
-    <repository owner="devteam" name="join" changeset_revision="11a49f94d086" description="Join the intervals of two datasets side-by-side">
+    <repository owner="devteam" name="join" changeset_revision="de21bdbb8d28" description="Join the intervals of two datasets side-by-side">
         <tool id="gops_join_1" version="1.0.0" file="new_operations/join.xml" />
     </repository>
     <repository owner="devteam" name="linear_regression" changeset_revision="cf431604ec3e" description="Perform Linear Regression">
@@ -63,7 +63,7 @@
     <repository owner="devteam" name="maf_cpg_filter" changeset_revision="7f2a12cb047d" description="Mask CpG/non-CpG sites from MAF file">
         <tool id="cpgFilter" version="1.0.0" file="regVariation/maf_cpg_filter.xml" />
     </repository>
-    <repository owner="devteam" name="merge" changeset_revision="55e88307811d" description="Merge the overlapping intervals of a dataset">
+    <repository owner="devteam" name="merge" changeset_revision="1bc76ceffa7f" description="Merge the overlapping intervals of a dataset">
         <tool id="gops_merge_1" version="1.0.0" file="new_operations/merge.xml" />
     </repository>
     <repository owner="devteam" name="microsats_alignment_level" changeset_revision="7852385470f3" description="Extract Orthologous Microsatellites from pair-wise alignments">
@@ -93,13 +93,13 @@
     <repository owner="devteam" name="substitutions" changeset_revision="c54f5d0bbb58" description="Fetch substitutions from pairwise alignments">
         <tool id="substitutions1" version="1.0.0" file="regVariation/substitutions.xml" />
     </repository>
-    <repository owner="devteam" name="subtract" changeset_revision="7bf44b9d7a8b" description="Subtract the intervals of two datasets">
+    <repository owner="devteam" name="subtract" changeset_revision="c19a2a29c561" description="Subtract the intervals of two datasets">
         <tool id="gops_subtract_1" version="1.0.0" file="new_operations/subtract.xml" />
     </repository>
     <repository owner="devteam" name="subtract_query" changeset_revision="5f6ebef89722" description="Subtract Whole Dataset from another dataset">
         <tool id="subtract_query1" version="0.1" file="new_operations/subtract_query.xml" />
     </repository>
-    <repository owner="devteam" name="table_recalibration" changeset_revision="53dd1bfced54" description="Table Recalibration on BAM files">
+    <repository owner="devteam" name="table_recalibration" changeset_revision="30e1dd77e99c" description="Table Recalibration on BAM files">
         <tool id="gatk_table_recalibration" version="0.0.5" file="gatk/table_recalibration.xml" />
     </repository>
     <repository owner="devteam" name="tables_arithmetic_operations" changeset_revision="82fa5062d611" description="Arithmetic Operations on tables">