Mercurial > repos > yating-l > gonramp_apollo_tools
diff jbrowsehubToApollo.xml @ 2:4be6fcac4bf2 draft default tip
planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894
| author | yating-l |
|---|---|
| date | Wed, 29 Nov 2017 15:39:32 -0500 |
| parents | 1da8b9042af4 |
| children |
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--- a/jbrowsehubToApollo.xml Tue Nov 28 12:43:22 2017 -0500 +++ b/jbrowsehubToApollo.xml Wed Nov 29 15:39:32 2017 -0500 @@ -11,7 +11,7 @@ </stdio> <command detect_errors="exit_code"><![CDATA[ - + mkdir -p $output.extra_files_path; ## Dump the tool parameters into a JSON file python $json_file parameters.json; python $__tool_directory__/jbrowsehubToApollo.py --data_json parameters.json -o $output @@ -24,11 +24,13 @@ file_path = sys.argv[1] #set global data_parameter_dict = {} #silent $data_parameter_dict.update({"action": str($action)}) +#silent $data_parameter_dict.update({"action": str($action)}) #silent $data_parameter_dict.update({"species_name": str($species_name)}) #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)} #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin}) #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)}) -#silent $data_parameter_dict.update({"extra_files_path": str($jbrowse_hub.extra_files_path)}) +#silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)}) +#slient $data_parameter_dict.update({"jbrowse_hub": str($jbrowse_hub.extra_files_path)}) #silent $data_parameter_dict.update({"port": str($advanced_options.port)}) #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)}) with open(file_path, 'w') as f: