Commit 59550112 authored by Penom Nom's avatar Penom Nom
Browse files

Fix bug with command line.

parent 65f5a594
......@@ -51,9 +51,10 @@ class Cdhit (Component):
# Files
self.input_fasta = InputFileList(input_fasta)
self.output_files = OutputFileList( self.get_outputs('nonRedundant.fasta', self.input_fasta), Formats.FASTA )
self.output_files = OutputFileList( self.get_outputs('{basename_woext}_nonRedundant.fasta', self.input_fasta), Formats.FASTA )
self.cluster_files = OutputFileList( self.get_outputs('{basename_woext}_nonRedundant.fasta.clstr', self.input_fasta) )
self.stderr = OutputFileList( self.get_outputs('{basename_woext}.stderr', self.input_fasta) )
def process(self):
cdhit = ShellFunction( self.get_exec_path("cd-hit") + " -i $1 -o $2 " + self.options + " 2> $3", '{EXE} {IN} {OUT}' )
cdhit = MultiMap( cdhit, inputs=self.input_fasta, outputs=[self.output_files, self.stderr] )
\ No newline at end of file
cdhit = ShellFunction( self.get_exec_path("cd-hit") + " -i $1 -o $2 " + self.options + " 2> $3", cmd_format='{EXE} {IN} {OUT}' )
cdhit = MultiMap( cdhit, inputs=self.input_fasta, outputs=[self.output_files, self.stderr, self.cluster_files] )
\ No newline at end of file
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