# HG changeset patch
# User eduardo
# Date 1497726653 14400
# Node ID 3302f18f9e16b82965d21d39de20cdc938df5862
# Parent  31e855c959361ccfc498f37807ae8500d765f816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty

diff -r 31e855c95936 -r 3302f18f9e16 annotateviz.py
--- a/annotateviz.py	Sat Jun 17 14:43:40 2017 -0400
+++ b/annotateviz.py	Sat Jun 17 15:10:53 2017 -0400
@@ -19,6 +19,7 @@
         parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=__doc__)
         parser.add_argument('-d','--database', help="gffutils sqlite database")
         parser.add_argument('-j','--json', help="report in json format")
+        args = parser.parse_args(argv)
         gffutils.constants.always_return_list = False
         db = gffutils.interface.FeatureDB(args.database)
         prediction_list = []
@@ -28,3 +29,5 @@
         add_matches(db.features_of_type("PFAM"), prediction_list)
         fout=open(args.json, 'w')
         json.dump(prediction_list,fout)
+if __name__ == "__main__":
+        main(sys.argv[1:],sys.stdout)
diff -r 31e855c95936 -r 3302f18f9e16 annotateviz.xml
--- a/annotateviz.xml	Sat Jun 17 14:43:40 2017 -0400
+++ b/annotateviz.xml	Sat Jun 17 15:10:53 2017 -0400
@@ -14,11 +14,10 @@
 --outdir $output.files_path
 $trackxml &&
 ##  $output.files_path/index.html $output;
-python  $__tool_directory__/annotateviz.py $db > $__tool_directory__/trans.json &&
+python  $__tool_directory__/annotateviz.py -d $db -j ${output.files_path}/trans.json &&
 sed "s@input_db@${__app__.security.encode_id($db.id)}@" $__tool_directory__/static/trinotateviz.html > $output &&
 cp $__tool_directory__/static/js/gff_app.js ${output.files_path} &&
-cp $__tool_directory__/static/css/main.css ${output.files_path} &&
-cp $__tool_directory__/trans.json ${output.files_path};
+cp $__tool_directory__/static/css/main.css ${output.files_path};
 ]]></command>
   <configfiles>
       <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>