# HG changeset patch
# User iuc
# Date 1443822847 14400
# Node ID d54881c558b833bfe7a22362188a5f167a714c86
# Parent  aa76a7fa6f821971845e4911e66dac901573a210
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty

diff -r aa76a7fa6f82 -r d54881c558b8 deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Sep 22 13:18:01 2015 -0400
+++ b/deepTools_macros.xml	Fri Oct 02 17:54:07 2015 -0400
@@ -242,7 +242,7 @@
             </param>
             <when value="cached">
                 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-                    <options from_data_table="deepTools_seqs">
+                    <options from_data_table="lastz_seqs">
                         <filter type="sort_by" column="1" />
                         <validator type="no_options" message="No indexes are available." />
                     </options>
diff -r aa76a7fa6f82 -r d54881c558b8 repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Fri Oct 02 17:54:07 2015 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories>
+    <repository changeset_revision="26e3ae5f74ed" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+</repositories>
diff -r aa76a7fa6f82 -r d54881c558b8 tool-data/deepTools_seqs.loc.sample
--- a/tool-data/deepTools_seqs.loc.sample	Tue Sep 22 13:18:01 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of 2bit genome files for use with deepTools. You will
-#need to supply these files and then create a deepTools_seqs.loc file
-#similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The deepTools_seqs.loc
-#file has this format:
-#
-#<unique_build_id>	<display_name>	<file_path>
-#
-#So, for example, if your deepTools_seqs.loc began like this:
-#
-#hg18	Human (Homo sapiens): hg18	/depot/data2/galaxy/twobit/hg18.2bit
-#hg19	Human (Homo sapiens): hg19	/depot/data2/galaxy/twobit/hg19.2bit
-#mm9	Mouse (Mus musculus): mm9	/depot/data2/galaxy/twobit/mm9.2bit
-#
-#then your /depot/data2/galaxy/twobit/ directory
-#would need to contain the following 2bit files:
-#
-#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.2bit
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.2bit
-#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 mm9.2bit
-#
-#Your deepTools_seqs.loc file should include an entry per line for 
-#each file you have stored that you want to be available. Note that 
-#your files should all have the extension '2bit'.
-#
-#Please note that the <unique_build_id> is also used as "Species name abbreviation".
diff -r aa76a7fa6f82 -r d54881c558b8 tool-data/lastz_seqs.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/lastz_seqs.loc.sample	Fri Oct 02 17:54:07 2015 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of 2bit genome files for use with deepTools. 
+#This file is named lastz_seqs.loc file to make use of an already existing loc
+#file from the lastz tool that is created by the twobit data-manager.
+#You will need to supply these files and then create a lastz_seqs.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The lastz_seqs.loc
+#file has this format:
+#
+#<unique_build_id>	<display_name>	<file_path>
+#
+#So, for example, if your lastz_seqs.loc began like this:
+#
+#hg18	Human (Homo sapiens): hg18	/depot/data2/galaxy/twobit/hg18.2bit
+#hg19	Human (Homo sapiens): hg19	/depot/data2/galaxy/twobit/hg19.2bit
+#mm9	Mouse (Mus musculus): mm9	/depot/data2/galaxy/twobit/mm9.2bit
+#
+#then your /depot/data2/galaxy/twobit/ directory
+#would need to contain the following 2bit files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.2bit
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.2bit
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 mm9.2bit
+#
+#Your lastz_seqs.loc file should include an entry per line for 
+#each file you have stored that you want to be available. Note that 
+#your files should all have the extension '2bit'.
+#
+#Please note that the <unique_build_id> is also used as "Species name abbreviation".
diff -r aa76a7fa6f82 -r d54881c558b8 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Tue Sep 22 13:18:01 2015 -0400
+++ b/tool_data_table_conf.xml.sample	Fri Oct 02 17:54:07 2015 -0400
@@ -1,7 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
 <tables>
-    <!-- Locations of 2bit sequence files for use in deepTools -->
-    <table name="deepTools_seqs" comment_char="#">
+    <!-- Locations of 2bit sequence files for use in Lastz -->
+    <table name="lastz_seqs" comment_char="#">
         <columns>value, name, path</columns>
-        <file path="tool-data/deepTools_seqs.loc" />
+        <file path="tool-data/lastz_seqs.loc" />
     </table>
 </tables>
diff -r aa76a7fa6f82 -r d54881c558b8 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 22 13:18:01 2015 -0400
+++ b/tool_dependencies.xml	Fri Oct 02 17:54:07 2015 -0400
@@ -4,6 +4,6 @@
         <repository changeset_revision="94e61bd56e40" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deepTools" version="1.5.11">
-        <repository changeset_revision="0eaccc10220c" name="package_python_2_7_deeptools_1_5_11" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="6fe93c81bcd0" name="package_python_2_7_deeptools_1_5_11" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>