Commit 2d136bce authored by Jerome Mariette's avatar Jerome Mariette
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parent 823b8139
......@@ -27,27 +27,41 @@ class Alignment (Workflow):
return "align reads against a reference genome"
def define_parameters(self, parameters_section=None):
self.add_input_file("read_1", "Which read1 files should be used", required=True, type="localfile", is_list=True)
self.add_input_file("read_1", "Which read1 files should be used", required=True, is_list=True)
self.add_input_file("read_2", "Which read2 files should be used (if single end, leave empty)", type="localfile", is_list=True)
self.add_input_file("reference_genome", "Which genome should the read being align on", required=True, type="localfile")
self.add_multiple_parameter("test", "toto est dnas le gazon", required=True)
self.add_input_file("toto", "Whices should be used", required=True, is_list=True, add_to="test")
self.add_input_file("tot_2", "Whould be used", type="int", add_to="test")
self.add_parameter("toto", "Whices should be used", required=True, is_list=True, add_to="test")
self.add_parameter("tot_2", "Whould be used", type="int", add_to="test")
self.add_parameter("rdate", "date be used", type="date", add_to="test")
self.add_exclusion_rule("read_1", "read_2")
self.add_exclusion_rule("toto", "tot_2")
self.add_multiple_parameter("unmulti", "unmulti qui fait chier", required=True, is_list=True)
self.add_parameter("a", "Wa", required=True, add_to="unmulti")
self.add_parameter("b", "Wb", type="int", add_to="unmulti")
self.add_parameter("c", "dc", type="date", add_to="unmulti")
#self.add_exclusion_rule("read_1", "read_2")
#self.add_exclusion_rule("toto", "tot_2")
def process(self):
#print self.read_1
#print self.read_2
#print self.reference_genome
#print self.test
# - supprimer les raise > mettre dans le log
# - handle inputfile url and so on ...
print self.read_1
print self.read_2
print self.reference_genome
print self.test
print self.unmulti
# index the reference genome
#bwaindex = self.add_component("BWAIndex", [self.args["reference_genome"]])
# align reads against indexed genome
#bwa = self.add_component("BWA", [bwaindex.databank, self.args["read_1"], self.args["read_2"]])
\ No newline at end of file
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