Question: Database Function
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gravatar for La Chi
6.6 years ago by
La Chi60
La Chi60 wrote:
hi , i have created a script which calls a database function(sub_id) and this function returns multiple columns , say its return 12 columns in database , but when i created its tool(function) in galaxy , i am able to return only 1 column(username) in galaxy tool which is not desirable result for me. i want to know how can i return all column from my database function(sub_id) and print its result in separate file(bed format) which should be shown history panel , here is my code function.py file import sys, os.path, logging from galaxy import eggs import pkg_resources from galaxy.model import * from sqlalchemy import * def load_db_values():     pkg_resources.require( "psycopg2" )     engine = create_engine('postgresql://postgres:@132.100.1.1:5432/users')     connection = engine.connect()     result_set = connection.execute( "select * from sub_id(5,10,10)" )     db = []     for row in result_set:         db += [(row ['username'],str(row[ 'userid' ]), False),]           connection.close()     return db def __main__():     columns = [int(x) for x in sys.argv[1].strip().split(',')]     for col in columns:         print col if __name__ == "__main__": __main__() function.xml file <tool id="FA" name="function" version="2.0.0">   <description>function</description>   <command interpreter="python">function.py $cols </command>     <inputs>     <param name="cols" type="select" multiple="true" display="checkboxes"    ="" label="Start" help="any help" dynamic_options="load_db_values()"    =""  ="">     <validator type="no_options" message="You must pick at least one value."/>     </param>   </inputs>  <outputs>    <data format="bed" name="out_file1"  =""/>   </outputs> </tool> function.py and function.xml files are located in galaxy- dist/tools/user tool_config <section name="Function" id="FA">
galaxy • 649 views
ADD COMMENTlink written 6.6 years ago by La Chi60
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