--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Wed Nov 28 14:20:39 2018 -0500
@@ -0,0 +1,170 @@
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--- a/README.rst	Wed Apr 12 17:44:58 2017 -0400
+++ b/README.rst	Wed Nov 28 14:20:39 2018 -0500
@@ -3,7 +3,7 @@
 
 This is a modified Galaxy wrapper for regtools which is based on the previous wrapper written by Remi Marenco (https://github.com/remimarenco/regtools). "regtools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context" (https://regtools.readthedocs.io/en/latest/).
 
-This wrapper adds an validation step to check if the output files are valid BED format. The lines with invalid strand (neighter "+" or "-") will be removed. 
+This wrapper adds an validation step to check if the output files are valid BED format. The lines with invalid strand (neither "+" or "-") will be removed. 
 
 This wrapper creates a new 13th column to store the scores. The scores in column 4 will be changed to 1000. 
 

--- a/regtools_junctions_extract.xml	Wed Apr 12 17:44:58 2017 -0400
+++ b/regtools_junctions_extract.xml	Wed Nov 28 14:20:39 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="regtools_junctions_extract" name="regtools junctions extract" version="0.1.0">
+<tool id="regtools_junctions_extract" name="regtools junctions extract" version="0.1.1">
     <description>Extract splice junctions from a RNA-Seq BAM file</description>
     <requirements>
-        <requirement type="package" version="0.3.0">regtools</requirement>
+        <requirement type="package" version="0.5.0">regtools</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />

--- a/tool_dependencies.xml	Wed Apr 12 17:44:58 2017 -0400
+++ b/tool_dependencies.xml	Wed Nov 28 14:20:39 2018 -0500
@@ -1,19 +1,17 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
-    <package name="regtools" version="0.3.0">
+    <package name="regtools" version="0.5.0">
         <install version="1.0">
             <actions>
-                <action type="shell_command">git clone --recursive https://github.com/griffithlab/regtools.git</action>
+                <action type="shell_command">git clone http://github.com/griffithlab/regtools --recursive -b 0.5.0</action>
                 <action type="make_directory">build</action>
                 <action type="change_directory">build</action>
-
                 <action type="set_environment_for_install">
                     <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="cmake" version="3.2.3" />
+                        <package name="cmake" version="3.2.3"/>
                     </repository>
                 </action>
                 <action type="shell_command">cmake ..</action>
-
                 <action type="shell_command">make</action>
                 <action type="move_file">
                     <source>regtools</source>
@@ -25,4 +23,4 @@
             </actions>
         </install>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file