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########################################################################################
# #
# Author: Herve Menager, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
from Mobyle.Workflow import Workflow, Task, Link, Parameter, Type, Datatype, Biotype, Parser #@UnusedImport
print __file__
if __name__ == "__main__":
wf = Workflow()
wf.name = 'toto'
wf.version = '1.1'
wf.title = 'test workflow'
wf.description = 'this workflow is a test one'
t1 = Task()
t1.id = 1
t1.service = 'clustalw-multialign'
t1.suspend = False
t1.description = "Run a clustalw"
t2 = Task()
t2.id = 2
t2.service = 'protdist'
t2.suspend = True
t2.description = "Run a protdist"
input = Parameter()
input.id = '1'
input.name = 'sequences'
input.prompt = 'Input sequences'
input.type = Type()
input.type.datatype = Datatype()
input.type.datatype.class_name = "Sequence"
input.type.biotypes = [Biotype("Protein")]
output_format = Parameter()
output_format.id = '2'
output_format.name = 'alignment_format'
output_format.prompt = 'Alignment format'
output_format.type = Type()
output_format.type.datatype = Datatype()
output_format.type.datatype.class_name = "String"
output = Parameter()
output.id = '3'
output.isout = True
output.name = 'matrix'
output.prompt = 'Distance matrix'
output.type = Type()
output.type.datatype = Datatype()
output.type.datatype.class_name = "Matrix"
output.type.datatype.superclass_name = "AbstractText"
output.type.biotypes = [Biotype("Protein")]
l1 = Link()
l1.to_task = t1.id
l1.from_parameter = "1"
l1.to_parameter = "infile"
l2 = Link()
l2.to_task = t1.id
l2.from_parameter = "2"
l2.to_parameter = "outputformat"
l3 = Link()
l3.from_task = t1.id
l3.to_task = t2.id
l3.from_parameter = "aligfile"
l3.to_parameter = "infile"
l4 = Link()
l4.from_task = t2.id
l4.from_parameter = "outfile"
l4.to_parameter = "3"
wf.tasks = [t1, t2]
wf.links = [l1, l2, l3, l4]
wf.parameters = [input, output_format, output]
mp = Parser()
print mp.tostring(wf)
wffile = open( '/tmp/workflow.xml', 'w' )
wffile.write( mp.tostring(wf))
wffile.close()
print mp.parse('/tmp/workflow.xml')
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