Commit e16e1ca7 authored by Penom Nom's avatar Penom Nom
Browse files

maj

parent bfb70b03
......@@ -54,11 +54,10 @@ class MothurChimeraUchime(Component):
self.stderr = OutputFileList(self.get_outputs('{basename_woext}.stderr', self.fasta_files))
def process(self):
if self.reference_files:
if self.reference_files and not self.names_files and not self.groups_files:
chimerauchime = ShellFunction(self.get_exec_path("mothur") + ' "#chimera.uchime(fasta=$1,reference=$2,outputdir='+self.output_directory+\
'/,processors='+str(self.processors)+')" > $3 2>$4', cmd_format='{EXE} {IN} {OUT}')
chimerauchime = MultiMap(chimerauchime, inputs=[self.fasta_files,self.reference_files], \
outputs=[self.stdout,self.stderr,self.uchime_chimera_files,self.uchime_accnos_files])
'/,processors='+str(self.processors)+')" > $2 2>$3', cmd_format='{EXE} {IN} {OUT}')
chimerauchime = MultiMap(chimerauchime, inputs=[self.fasta_files], outputs=[self.stdout,self.stderr,self.uchime_chimera_files,self.uchime_accnos_files])
elif self.names_files and not self.groups_files:
chimerauchime = ShellFunction(self.get_exec_path("mothur") + ' "#chimera.uchime(fasta=$1,name=$2,outputdir='+self.output_directory+\
'/,processors='+str(self.processors)+')" > $3 2>$4', cmd_format='{EXE} {IN} {OUT}')
......
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