reference_assemble_sanger_sequences

--alignment-stringency
<[LOW, MEDIUM,HIGH]> A higher stringency level will tend to produce contigs with less ambiguities but will also tend to omit more sequencing reads and to generate more and shorter contigs (default: MEDIUM)
--conflicts <[VOTE, UNKNOWN, AMBIGUTY]> conflicts (default: VOTE)
-d, --destination <ClcServerObjectUrl> Destination file or folder on server. If not specified the folder of the first input object will be used.
-i, --input <ClcObjectUrl> Input data on server
--include-partly <Boolean> Remove ends of the reference sequence that do not align with any reads (default: false)
--include-reference
<[INCLUDE_REFERENCE, EXCLUDE_REFERENCE]
> Whether to include reference sequence in contig(s) or not (default: INCLUDE_REFERENCE)
--install-consensus <Boolean> install-consensus (default: true)
--log <Boolean> Enable creation of algo log file. (default: true)
--min-length
Integer: 1 <= x <= 2147483647 Exclude reads if less than this number of nucleotides can be aligned to the contig (default: 50)
--reference <ClcObjectUrl> Reference sequences or genome track
--reference-given <Boolean> reference-given (default: true)
--residues <Integer> The number of overhanging residues to keep from the reference sequence (default: 100)
--use-trim <Boolean> Exclude regions of sequencing reads which have previously been trimmed (default: false)