Commit 29b205e1 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

some updates on r454_diversity

parent 1a1f704d
......@@ -19,10 +19,28 @@ class MothurTrimSeqs(Component):
minlength=200, maxlength=600, bdiffs=0, pdiffs=2, processors=1):
"""
Define shh.flows component parameters.
:param flow_file: a flow file to process
:param fasta_files: fasta files to process
:type sff_files: str
:param processors: the number of processors to use
:type processors: int
:param names_files: names files to process
:type names_files: str
:param oligos_file: the oligos file where are stored fwd/rvrs primers and barecodes
:type oligos_file: str
:param flip: should sequences be oriented
:type flip: bool
:param qaverage: remove sequences that have an average below the value provided
:type qaverage: int
:param maxambig: cull sequences with have ambiguous bases
:type maxambig: int
:param maxhomop: cap the homopolymer length
:type maxhomop: int
:param minlength: discared sequences too short
:type minlength: int
:param maxlength: discared sequences too long
:type maxlength: int
:param bdiffs: the maximum number of differences allowed with the barecode
:type bdiffs: int
:param pdiffs: the maximum number of differences allowed with the primer
:type pdiffs: int
"""
# define parameters
self.processors = processors
......
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