# HG changeset patch
# User yating-l
# Date 1493844729 14400
# Node ID 2804b5f00dc76ffcb192167849ee470d5b5e7d9e
# Parent  c4737db26737776309cace176da4f2a7783282b2
planemo upload

diff -r c4737db26737 -r 2804b5f00dc7 data_manager/fetch_reference_data.py
--- a/data_manager/fetch_reference_data.py	Wed May 03 16:32:05 2017 -0400
+++ b/data_manager/fetch_reference_data.py	Wed May 03 16:52:09 2017 -0400
@@ -53,9 +53,10 @@
 def main():
     #Parse Command Line
     parser = argparse.ArgumentParser()
+    parser.add_argument('-o', '--out', help='Output file')
     args = parser.parse_args()
 
-    filename = args[0]
+    filename = args.out
 
     params = from_json_string(open(filename).read())
     target_directory = params['output_data'][0]['extra_files_path']
diff -r c4737db26737 -r 2804b5f00dc7 data_manager/fetch_reference_data.xml
--- a/data_manager/fetch_reference_data.xml	Wed May 03 16:32:05 2017 -0400
+++ b/data_manager/fetch_reference_data.xml	Wed May 03 16:52:09 2017 -0400
@@ -1,6 +1,6 @@
 <tool id="data_manager_fetch_reference_data" name="Reference data for GlimmerHMM" version="0.0.1" tool_type="manage_data">
     <description>fetching reference data for GlimmerHMM</description>
-    <command interpreter="python">fetch_reference_data.py "${out_file}"</command>
+    <command interpreter="python">fetch_reference_data.py -o "${out_file}"</command>
     <inputs>
         <param name="genome_id" type="text" label="Id of the reference genome" />
         <param name="genome_name" type="text" label="Name of the reference genome" />