Mercurial > repos > yating-l > gonramp_apollo_tools

comparison jbrowsehubToApollo.xml @ 2:4be6fcac4bf2 draft default tip

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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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1:78af01d73add 2:4be6fcac4bf2
9 9
10 <stdio> 10 <stdio>
11 </stdio> 11 </stdio>
12 12
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 14 mkdir -p $output.extra_files_path;
15 ## Dump the tool parameters into a JSON file 15 ## Dump the tool parameters into a JSON file
16 python $json_file parameters.json; 16 python $json_file parameters.json;
17 python $__tool_directory__/jbrowsehubToApollo.py --data_json parameters.json -o $output 17 python $__tool_directory__/jbrowsehubToApollo.py --data_json parameters.json -o $output
18 ]]></command> 18 ]]></command>
19 <configfiles> 19 <configfiles>
22 import sys 22 import sys
23 23
24 file_path = sys.argv[1] 24 file_path = sys.argv[1]
25 #set global data_parameter_dict = {} 25 #set global data_parameter_dict = {}
26 #silent $data_parameter_dict.update({"action": str($action)}) 26 #silent $data_parameter_dict.update({"action": str($action)})
27 #silent $data_parameter_dict.update({"action": str($action)})
27 #silent $data_parameter_dict.update({"species_name": str($species_name)}) 28 #silent $data_parameter_dict.update({"species_name": str($species_name)})
28 #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)} 29 #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)}
29 #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin}) 30 #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin})
30 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)}) 31 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
31 #silent $data_parameter_dict.update({"extra_files_path": str($jbrowse_hub.extra_files_path)}) 32 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
33 #slient $data_parameter_dict.update({"jbrowse_hub": str($jbrowse_hub.extra_files_path)})
32 #silent $data_parameter_dict.update({"port": str($advanced_options.port)}) 34 #silent $data_parameter_dict.update({"port": str($advanced_options.port)})
33 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)}) 35 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
34 with open(file_path, 'w') as f: 36 with open(file_path, 'w') as f:
35 json.dump($data_parameter_dict, f) 37 json.dump($data_parameter_dict, f)
36 </configfile> 38 </configfile>