Mercurial > repos > yating-l > gonramp_apollo_tools

comparison apolloUserManager.xml @ 1:78af01d73add draft

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planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
author yating-l
date Tue, 28 Nov 2017 12:43:22 -0500
parents 1da8b9042af4
children
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0:1da8b9042af4 1:78af01d73add
12 12
13 <stdio> 13 <stdio>
14 </stdio> 14 </stdio>
15 15
16 <command detect_errors="exit_code"><![CDATA[ 16 <command detect_errors="exit_code"><![CDATA[
17 17 mkdir -p $output.extra_files_path;
18 ## Dump the tool parameters into a JSON file 18 ## Dump the tool parameters into a JSON file
19 python $json_file parameters.json; 19 python $json_file parameters.json;
20 python $__tool_directory__/apolloUserManager.py --data_json parameters.json -o $output 20 python $__tool_directory__/apolloUserManager.py --data_json parameters.json -o $output
21 ]]></command> 21 ]]></command>
22 <configfiles> 22 <configfiles>
90 90
91 91
92 #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)} 92 #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)}
93 #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin}) 93 #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin})
94 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)}) 94 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
95 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
95 #silent $data_parameter_dict.update({"port": str($advanced_options.port)}) 96 #silent $data_parameter_dict.update({"port": str($advanced_options.port)})
96 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)}) 97 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
97 with open(file_path, 'w') as f: 98 with open(file_path, 'w') as f:
98 json.dump($data_parameter_dict, f) 99 json.dump($data_parameter_dict, f)
99 </configfile> 100 </configfile>
234 </param> 235 </param>
235 </when> 236 </when>
236 </conditional> 237 </conditional>
237 </inputs> 238 </inputs>
238 <outputs> 239 <outputs>
239 <data format="html" name="output" label="${tool.name}" /> 240 <data format="txt" name="output" label="${tool.name} on ${on_string}" />
240 </outputs> 241 </outputs>
241 242
242 <help> 243 <help>
243 This Galaxy tool is used to manage Apollo users.The currently supported operation including: 244 This Galaxy tool is used to manage Apollo users.The currently supported operation including:
244 245