Commit 8e0c637d authored by Penom Nom's avatar Penom Nom
Browse files

maj

parent e16e1ca7
......@@ -47,13 +47,13 @@ class MothurAlignSeqs(Component):
self.processors = processors
# define input files
self.fasta_files = InputFileList(fasta_files, Formats.FASTA)
self.reference_alignment_files = InputFileList(reference_alignment_files, Formats.FASTA)
self.reference_alignment_files = InputFile(reference_alignment_files, Formats.FASTA)
# define output files
self.align_files = OutputFileList(self.get_outputs('{basename_woext}.align', self.fasta_files), Formats.FASTA)
self.align_report_files = OutputFileList(self.get_outputs('{basename_woext}.align.report', self.fasta_files))
self.stdout = OutputFileList(self.get_outputs('{basename_woext}.stdout', self.fasta_files))
def process(self):
alignseqs = ShellFunction(self.get_exec_path("mothur") + ' "#align.seqs(fasta=$1,reference=$2,outputdir='+self.output_directory + \
'/,processors='+str(self.processors)+')" > $3', cmd_format='{EXE} {IN} {OUT}')
alignseqs = MultiMap(alignseqs, inputs=[self.fasta_files,self.reference_alignment_files], outputs=[self.stdout,self.align_files,self.align_report_files])
alignseqs = ShellFunction(self.get_exec_path("mothur") + ' "#align.seqs(fasta=$1,reference='+self.reference_alignment_files+',outputdir='+self.output_directory + \
'/,processors='+str(self.processors)+')" > $2', cmd_format='{EXE} {IN} {OUT}')
alignseqs = MultiMap(alignseqs, inputs=[self.fasta_files], outputs=[self.stdout,self.align_files,self.align_report_files])
......@@ -41,7 +41,7 @@ class MothurChimeraUchime(Component):
self.processors = processors
#define input files
self.fasta_files = InputFileList(fasta_files, Formats.FASTA)
if reference_files : self.reference_files = InputFile(reference_files)
if reference_files : self.reference_files = InputFile(reference_files, Formats.FASTA)
else : self.reference_files = None
if names_files : self.names_files = InputFileList(names_files, Formats.MOTHUR_NAMES)
else : self.names_files = None
......@@ -55,7 +55,7 @@ class MothurChimeraUchime(Component):
def process(self):
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+\
chimerauchime = ShellFunction(self.get_exec_path("mothur") + ' "#chimera.uchime(fasta=$1,reference='+self.reference_files+',outputdir='+self.output_directory+\
'/,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:
......
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