root/galaxy-central/tools/rgenetics/rgfakePhe_code.py

# before running the qc, need to rename various output files
import os, string, time
from galaxy import datatypes
from galaxy import app
import galaxy.util

#Provides Upload tool with access to list of available builds
repospath = '/usr/local/galaxy/data/rg'
builds = []
#Read build names and keys from galaxy.util
for dbkey, build_name in galaxy.util.dbnames:
    builds.append((build_name,dbkey,False))

def timenow():
    """return current time as a string
    """
    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))

#Return available builds
def get_available_builds(defval='hg18'):
    for i,x in enumerate(builds):
        if x[1] == defval:
           x = list(x)
           x[2] = True
           builds[i] = tuple(x)
    return builds

# Create link to files here
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
    base_name = param_dict.get( 'title1', 'Null_Phenotype' )
    base_name = base_name.encode()
    info = 'Null phenotypes created by rgfakePhe at %s' % timenow()
    s = string.whitespace + string.punctuation
    ptran =  string.maketrans(s,'_'*len(s))
    base_name = base_name.translate(ptran)
    data = out_data['ppheout']
    data.name = '%s.phe' % (base_name) # that's how they've been named in rgfakePhe.py
    data.file_name = data.file_name
    data.metadata.base_name = base_name
    out_data['pheout'] = data
    app.model.context.flush()