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workflows/alignment/__init__.py

@@ -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):
-        pass
-        #print self.read_1
-        #print self.read_2
-        #print self.reference_genome
-        #print self.test
         
+        # TODO 
+        # - 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"]])
+        
+        
+        
+        
         
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