# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1398646623 18000
# Node ID b84716da559502b72999a5f4ed5ea6683116bfb2
# Parent  3cbbffb3ae4717613d74ae4f19d3f1cbece3fd9d
Update to SHEAR v0.2.9

diff -r 3cbbffb3ae47 -r b84716da5595 shear_assemble.xml
--- a/shear_assemble.xml	Thu Jan 30 15:53:55 2014 -0600
+++ b/shear_assemble.xml	Sun Apr 27 19:57:03 2014 -0500
@@ -1,7 +1,7 @@
-<tool id="shear_assemble" name="SHEAR-Assemble" version="0.0.7">
+<tool id="shear_assemble" name="SHEAR-Assemble" version="0.0.9">
   <description>create a personal genome from sdi</description>
   <requirements>
-    <requirement type="package" version="0.2.7">shear</requirement>
+    <requirement type="package" version="0.2.9">shear</requirement>
   </requirements>
   <!--
   <version_command></version_command>
@@ -58,5 +58,10 @@
   </tests>
   <help>
 SHEAR-Assemble takes a reference genome and a *.sdi file from SHEAR-SV to create a new personal genome.
+
+Please cite the following article:
+
+Landman SR, Hwang TH, Silverstein KAT, Li Y, Dehm SM, Steinbach M, and Kumar V. SHEAR: sample heterogeneity estimation and assembly by reference. BMC Genomics 2014, 15:84.
+
   </help>
 </tool>
diff -r 3cbbffb3ae47 -r b84716da5595 shear_sv.xml
--- a/shear_sv.xml	Thu Jan 30 15:53:55 2014 -0600
+++ b/shear_sv.xml	Sun Apr 27 19:57:03 2014 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="shear_sv" name="SHEAR-SV" version="0.0.7">
+<tool id="shear_sv" name="SHEAR-SV" version="0.0.9">
   <description>find SVs and estimate the heterogeneity levels from a BAM</description>
   <requirements>
-    <requirement type="package" version="0.2.7">shear</requirement>
+    <requirement type="package" version="0.2.9">shear</requirement>
     <requirement type="package" version="0.1.19">samtools</requirement>
     <requirement type="package" version="0.6.2">bwa</requirement>
     <requirement type="package" version="1.0.1">crest</requirement>
@@ -132,5 +132,10 @@
 heterogeneity level of those SVs. It will output a *.report file reporing the
 SVs and their heterogeneity levels, and it will output a *.sdi file that can be
 used for SHEAR-Assemble to reconstruct the new genome.
+
+Please cite the following article:
+
+Landman SR, Hwang TH, Silverstein KAT, Li Y, Dehm SM, Steinbach M, and Kumar V. SHEAR: sample heterogeneity estimation and assembly by reference. BMC Genomics 2014, 15:84.
+
   </help>
 </tool>
diff -r 3cbbffb3ae47 -r b84716da5595 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jan 30 15:53:55 2014 -0600
+++ b/tool_dependencies.xml	Sun Apr 27 19:57:03 2014 -0500
@@ -19,8 +19,8 @@
   Bioperl package Bio::DB:Sam  
           </readme>
     </package>
-    <package name="shear" version="0.2.7">
-        <repository changeset_revision="f64a3597da37" name="package_shear_0_2_7" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <package name="shear" version="0.2.9">
+        <repository changeset_revision="516ed9ae8174" name="package_shear_0_2_9" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
 
 </tool_dependency>