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> <code file="function.py" /> <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"> <tool file ="user/function.xml/> </section>
thanks