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60 lines
2.3 KiB
Python
60 lines
2.3 KiB
Python
import pkg_resources; pkg_resources.require( "bx-python" )
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from bx.align import maf
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from galaxy import datatypes, config, jobs
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from shutil import move
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def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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output_data = out_data.items()[0][1]
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history = output_data.history
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if history == None:
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print "unknown history!"
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return
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new_stdout = ""
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split_stdout = stdout.split("\n")
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basic_name = output_data.name
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output_data_list = []
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for line in split_stdout:
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if line.startswith("#FILE1"):
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fields = line.split("\t")
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dbkey = fields[1]
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filepath = fields[2]
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output_data.dbkey = dbkey
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output_data.name = basic_name + " (" + dbkey + ")"
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app.model.context.add( output_data )
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app.model.context.flush()
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output_data_list.append(output_data)
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elif line.startswith("#FILE"):
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fields = line.split("\t")
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dbkey = fields[1]
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filepath = fields[2]
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newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context )
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newdata.set_size()
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newdata.extension = "bed"
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newdata.name = basic_name + " (" + dbkey + ")"
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app.model.context.add( newdata )
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app.model.context.flush()
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history.add_dataset( newdata )
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app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset )
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app.model.context.add( history )
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app.model.context.flush()
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try:
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move(filepath,newdata.file_name)
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newdata.info = newdata.name
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newdata.state = newdata.states.OK
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except:
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newdata.info = "The requested file is missing from the system."
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newdata.state = newdata.states.ERROR
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newdata.dbkey = dbkey
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newdata.init_meta()
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newdata.set_meta()
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newdata.set_peek()
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app.model.context.flush()
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output_data_list.append(newdata)
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else:
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new_stdout = new_stdout + line
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for data in output_data_list:
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if data.state == data.states.OK:
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data.info = new_stdout
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app.model.context.add( data )
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app.model.context.flush()
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