import os import pkg_resources; pkg_resources.require( "bx-python" ) from bx.align import maf from galaxy import datatypes, config, jobs from shutil import move def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): output_data = out_data.items()[0][1] new_stdout = "" split_stdout = stdout.split("\n") for line in split_stdout: if line.startswith("#FILE1"): fields = line.split("\t") dbkey = fields[1] output_data.dbkey = dbkey output_data.name = "%s (%s)" % ( output_data.name, dbkey ) app.model.context.add( output_data ) app.model.context.flush() else: new_stdout = "%s\n%s" % ( new_stdout, line ) for data in output_data.creating_job.output_datasets: data = data.dataset data.info = new_stdout app.model.context.add( data ) app.model.context.flush()