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workflows/r454_diversity/components/mothurmakeshared.py

@@ -10,13 +10,17 @@ class MothurMakeShared(Component):
     Create a table that indicates the number of times an OTU shows up in each sample
     """
     
-    def define_parameters(self, an_list_files, groups_files):
+    def define_parameters(self, an_list_files, groups_files, label="unique-0.01"):
         """
         :param an_list_files: an list files to process
         :type an_list_files: str
         :param groups_files: groups files to process
         :type groups_files: str
+        :param label : 
+        :type label : str
         """
+        #define parameters
+        self.label = label
         #define input files
         self.an_list_files = InputFileList(an_list_files)
         self.groups_files = InputFileList(groups_files, Formats.MOTHUR_GROUPS)
@@ -25,5 +29,6 @@ class MothurMakeShared(Component):
         self.stdout = OutputFileList(self.get_outputs('{basename_woext}.stdout', self.an_list_files))
     def process(self):
         print ">>>Process make.shared"
-        makeshared = ShellFunction(self.get_exec_path("mothur") + ' "#make.shared(list=$1,group=$2,outputdir='+self.output_directory+'/)" > $3',cmd_format='{EXE} {IN} {OUT}')
+        makeshared = ShellFunction(self.get_exec_path("mothur") + ' "#make.shared(list=$1,group=$2,label='+self.label+',outputdir='+self.output_directory+'/)" > $3',\
+                                   cmd_format='{EXE} {IN} {OUT}')
         makeshared = MultiMap(makeshared, inputs=[self.an_list_files,self.groups_files], outputs=[self.stdout,self.an_shared_files])
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