# HG changeset patch
# User gbcs-embl-heidelberg
# Date 1498037013 14400
# Node ID 4ccf1406832de2d5f0774824c2f5cf49faf1f18a
# Parent  f6bc74863c1ce90b55fae5227dbd9deaf7c54211
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit dd9e62bdb01d1252a90ce778103ce9b6b4a8cd52-dirty

diff -r f6bc74863c1c -r 4ccf1406832d README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Jun 21 05:23:33 2017 -0400
@@ -0,0 +1,19 @@
+# HowTo update the toolshed repository
+
+After linting/testing your update using ``planemo test`` and ``planemo serve`` you can upload the changes to the toolshed repos.
+
+For this you need to have the credentials or api_key of our ``gbcs-embl-heidelberg`` user.
+To make it easier, put this information in your global ``~/.planemo.yml`` file. The format is described here: https://planemo.readthedocs.io/en/latest/configuration.html
+
+The commands below work due to the ``.shed.yml`` file in this directory.
+
+## Update testtoolshed
+
+``planemo shed_update --shed_target testtoolshed``
+
+Look at the result and then update the main toolshed.
+
+## Update toolshed
+
+``planemo shed_update --shed_target toolshed``
+
diff -r f6bc74863c1c -r 4ccf1406832d je
--- a/je	Wed Dec 07 11:57:09 2016 -0500
+++ b/je	Wed Jun 21 05:23:33 2017 -0400
@@ -1,11 +1,11 @@
 #!/bin/sh
-# Wrapper around je_1.0_bundle.jar
+# Wrapper around je_1.1_bundle.jar
 
 # where are we stored ?
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 # echo $DIR
 # path to jar file to execute, this jar is supposed to be in the same dir as this script
-JAR_FILE=$DIR"/je_1.0_bundle.jar"
+JAR_FILE=$DIR"/je_1.1_bundle.jar"
 
 # set default _JAVA_OPTIONS
 _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx4G -Xms256m'}
diff -r f6bc74863c1c -r 4ccf1406832d je-markdupes.xml
--- a/je-markdupes.xml	Wed Dec 07 11:57:09 2016 -0500
+++ b/je-markdupes.xml	Wed Jun 21 05:23:33 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="je_markdupes" name="Je-MarkDuplicates" version="1.0">
+<tool id="je_markdupes" name="Je-MarkDuplicates" version="@VERSION_STRING@">
     <description>to filter BAM files for read duplicates taking UMIs into account</description>
     <macros>
         <import>macros.xml</import>
diff -r f6bc74863c1c -r 4ccf1406832d je_1.0_bundle.jar
Binary file je_1.0_bundle.jar has changed
diff -r f6bc74863c1c -r 4ccf1406832d je_1.1_bundle.jar
Binary file je_1.1_bundle.jar has changed
diff -r f6bc74863c1c -r 4ccf1406832d macros.xml
--- a/macros.xml	Wed Dec 07 11:57:09 2016 -0500
+++ b/macros.xml	Wed Jun 21 05:23:33 2017 -0400
@@ -1,5 +1,7 @@
 <macros>
 
+    <token name="@VERSION_STRING@">1.1</token>
+
     <token name="@single_or_paired_cmd@">
         #if str( $library.type ) == "single":
             F1=${library.input_1}