Commit e0dd583d authored by Penom Nom's avatar Penom Nom
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parent 5b1ec377
......@@ -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])
\ No newline at end of file
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