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1 import pkg_resources; pkg_resources.require( "bx-python" )
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2 from bx.align import maf
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3 from galaxy import datatypes, config, jobs
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4 from shutil import move
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5
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6 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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7 output_data = out_data.items()[0][1]
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8 history = output_data.history
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9 if history == None:
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10 print "unknown history!"
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11 return
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12 new_stdout = ""
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13 split_stdout = stdout.split("\n")
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14 basic_name = output_data.name
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15 output_data_list = []
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16 for line in split_stdout:
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17 if line.startswith("#FILE1"):
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18 fields = line.split("\t")
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19 dbkey = fields[1]
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20 filepath = fields[2]
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21 output_data.dbkey = dbkey
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22 output_data.name = basic_name + " (" + dbkey + ")"
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23 app.model.context.add( output_data )
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24 app.model.context.flush()
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25 output_data_list.append(output_data)
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26 elif line.startswith("#FILE"):
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27 fields = line.split("\t")
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28 dbkey = fields[1]
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29 filepath = fields[2]
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30 newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context )
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31 newdata.set_size()
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32 newdata.extension = "bed"
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33 newdata.name = basic_name + " (" + dbkey + ")"
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34 app.model.context.add( newdata )
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35 app.model.context.flush()
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36 history.add_dataset( newdata )
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37 app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset )
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38 app.model.context.add( history )
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39 app.model.context.flush()
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40 try:
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41 move(filepath,newdata.file_name)
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42 newdata.info = newdata.name
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43 newdata.state = newdata.states.OK
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44 except:
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45 newdata.info = "The requested file is missing from the system."
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46 newdata.state = newdata.states.ERROR
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47 newdata.dbkey = dbkey
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48 newdata.init_meta()
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49 newdata.set_meta()
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50 newdata.set_peek()
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51 app.model.context.flush()
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52 output_data_list.append(newdata)
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53 else:
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54 new_stdout = new_stdout + line
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55 for data in output_data_list:
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56 if data.state == data.states.OK:
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57 data.info = new_stdout
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58 app.model.context.add( data )
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59 app.model.context.flush()
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