Commit cfb59259 authored by Penom Nom's avatar Penom Nom
Browse files

Fix bug with concatenation of parameter processor.

parent 17c09807
......@@ -27,7 +27,7 @@ class MothurClusterSplit(Component):
@summary : Assign sequences to OTUs in two step : splitting of your files into distinct groupings and the clustering of these groupings.
"""
def define_parameters(self, fasta_files, taxonomy_files, names_files=None, count_table_files=None, taxonomy_level=4, cutoff=None, method="average", processors=1):
def define_parameters(self, fasta_files, taxonomy_files, names_files=None, count_table_files=None, taxonomy_level=3, cutoff=None, method="average", processors=1):
"""
@param fasta_files : [string] Sequences processed.
@param taxonomy_files : [string] The taxonomy file for your sequences.
......@@ -75,9 +75,9 @@ class MothurClusterSplit(Component):
cutoff_option = ',cutoff='+str(self.cutoff)
if self.names_files :
cluster = ShellFunction(self.get_exec_path("mothur") + ' "#cluster.split(fasta=$1, name=$2, taxonomy=$3, outputdir=' + self.output_directory + '/' + cutoff_option +\
', taxlevel=' + str(self.tax_level) + ', method=' + self.method + ', splitmethod=' + self.split_method + ', processor=' + str(self.processors_nb) + ')" > $4',cmd_format='{EXE} {IN} {OUT}')
', taxlevel=' + str(self.tax_level) + ', method=' + self.method + ', splitmethod=' + self.split_method + ', processors=' + str(self.processors_nb) + ')" > $4',cmd_format='{EXE} {IN} {OUT}')
cluster = MultiMap(cluster, inputs=[self.fasta_files, self.names_files, self.taxonomy_files], outputs=[self.stdout, self.an_sabund_files, self.an_rabund_files, self.an_list_files])
if self.count_table_files :
cluster = ShellFunction(self.get_exec_path("mothur") + ' "#cluster.split(fasta=$1, count=$2, taxonomy=$3, outputdir=' + self.output_directory + '/' + cutoff_option +\
', taxlevel=' + str(self.tax_level) + ', method=' + self.method + ', splitmethod=' + self.split_method + ', processor=' + str(self.processors_nb) + ')" > $4',cmd_format='{EXE} {IN} {OUT}')
', taxlevel=' + str(self.tax_level) + ', method=' + self.method + ', splitmethod=' + self.split_method + ', processors=' + str(self.processors_nb) + ')" > $4',cmd_format='{EXE} {IN} {OUT}')
cluster = MultiMap(cluster, inputs=[self.fasta_files, self.count_table_files, self.taxonomy_files], outputs=[self.stdout, self.an_list_files])
\ No newline at end of file
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