mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Daniel Blankenberg
4cbfce361b
Datatypes are defined like: [galaxy:datatypes] bed = galaxy.datatypes.interval:Bed png = galaxy.datatypes.images:Image,image/png where the mime-type (default of text/plain) can be declared after the class name, as is seen with png.
45 lines
2.0 KiB
Python
45 lines
2.0 KiB
Python
#Code for direct connection to UCSC
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from galaxy import datatypes
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def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
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"""Sets the name of the data"""
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outputType = param_dict.get( 'hgta_outputType', "interval" ).lower() #assume all data is interval, we will fix later if not the case
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#list for converting ucsc to galaxy exts, if not in following dictionary, use provided datatype
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outputType_to_ext = {'wigdata':'wig','tab':'interval','hyperlinks':'html','sequence':'fasta'}
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items = out_data.items()
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description = param_dict.get('hgta_regionType',"")
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organism = param_dict.get('org',"unkown species")
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table = param_dict.get('hgta_track',"")
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if description == 'range':
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try:
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description = param_dict.get('position',"")
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except:
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description = "unkown position"
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for name, data in items:
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data.name = "%s on %s: %s (%s)" % (data.name, organism, table, description)
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data.dbkey = param_dict.get('db', '?')
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ext = outputType
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try: ext = outputType_to_ext[outputType]
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except: pass
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if ext not in app.datatypes_registry.datatypes_by_extension: ext = 'interval'
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data = app.datatypes_registry.change_datatype(data, ext)
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#store ucsc parameters temporarily in output file
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out = open(data.file_name,'w')
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for key, value in param_dict.items():
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print >> out, "%s\t%s" % (key,value)
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out.close()
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out_data[name] = data
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def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
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"""Verifies the datatype after the run"""
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name, data = out_data.items()[0]
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if data.state == data.states.OK: data.info = data.name
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if not isinstance(data.datatype, datatypes.interval.Bed) and isinstance(data.datatype, datatypes.interval.Interval):
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data.set_meta()
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if data.missing_meta(): data = app.datatypes_registry.change_datatype(data, 'tabular')
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data.set_peek()
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data.flush()
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