# HG changeset patch
# User iuc
# Date 1576684012 18000
# Node ID 3235aeb45c229f54e5c18d696e97e0c510a9062d
# Parent  9de82b4963e64b9e47ad46869eefbff13e8af156
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"

diff -r 9de82b4963e6 -r 3235aeb45c22 jbrowse-fromdir.xml
--- a/jbrowse-fromdir.xml	Wed Sep 11 09:40:36 2019 -0400
+++ b/jbrowse-fromdir.xml	Wed Dec 18 10:46:52 2019 -0500
@@ -7,12 +7,15 @@
   <command detect_errors="exit_code"><![CDATA[
 ## Create output directory
 mkdir -p $output.files_path &&
+
+export JBROWSE_SOURCE_DIR=\$(dirname \$(command -v prepare-refseqs.pl))/../opt/jbrowse  &&
+
 ## Copy in jbrowse
 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&
 
 ## Copy in data directory
 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
-mv $output.files_path/index.html $output
+cp $output.files_path/index.html $output
 ]]></command>
   <inputs>
     <param label="JBrowse Data Directory"
diff -r 9de82b4963e6 -r 3235aeb45c22 jbrowse.xml
--- a/jbrowse.xml	Wed Sep 11 09:40:36 2019 -0400
+++ b/jbrowse.xml	Wed Dec 18 10:46:52 2019 -0500
@@ -16,6 +16,8 @@
 ## but nice if users want to reproduce locally
 cp $trackxml $output.files_path/galaxy.xml &&
 
+export JBROWSE_SOURCE_DIR=\$(dirname \$(which prepare-refseqs.pl))/../opt/jbrowse  &&
+
 ## Once that's done, we run the python script to handle the real work
 python '$__tool_directory__/jbrowse.py'
 
@@ -28,14 +30,14 @@
 $trackxml &&
 
 #if str($standalone) == "Complete":
-    mv $output.files_path/index.html $output;
+    cp $output.files_path/index.html $output;
 #else:
-    mv $dummyIndex $output;
+    cp $dummyIndex $output;
 #end if
 
 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
 #if str($uglyTestingHack) == "enabled":
-    mv $trackxml $output
+    cp $trackxml $output
 #end if
   ]]></command>
   <configfiles>
diff -r 9de82b4963e6 -r 3235aeb45c22 macros.xml
--- a/macros.xml	Wed Sep 11 09:40:36 2019 -0400
+++ b/macros.xml	Wed Dec 18 10:46:52 2019 -0500
@@ -14,7 +14,7 @@
     </requirements>
   </xml>
   <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
-  <token name="@WRAPPER_VERSION@">galaxy5</token>
+  <token name="@WRAPPER_VERSION@">galaxy6</token>
   <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**