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sixgill build (version 0.2.4.0)
filters
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MetaGene Annotators
MetaGene Annotator 0
usage: sixgill_build [-h] [--minlength MINLENGTH]
[--minqualscore MINQUALSCORE] [--metagenefile METAGENEFILE] [--minmetagenescore MINMETAGENESCORE] [--minorflength MINORFLENGTH] [--minlongesttryppeplen MINLONGESTTRYPPEPLEN] [--maxreads MAXREADS] [--minreadcount MINREADCOUNT] --out OUT [--outfasta OUTFASTA] [--debug] fastqfiles [fastqfiles ...]

Read in one or more fastq files. For each read, do a 6-frame translation and add all metapeptides that pass the specified filtering criteria. If --metagenefile is specified, start with the output of MetaGene Annotator instead of raw reads.

positional arguments:
fastqfiles input fastq file(s), bgzipped
optional arguments:
-h, --help show this help message and exit
--minlength MINLENGTH
 min AA length of a metapeptide
--minqualscore MINQUALSCORE
 min base-call phred score across any NT in a metapeptide
--metagenefile METAGENEFILE
 input MetaGene Annotator output file. Records must be in same linear order as reads in fastqfiles
--minmetagenescore MINMETAGENESCORE
 minimum MetaGene score
--minorflength MINORFLENGTH
 min length of ORF-portion
--minlongesttryppeplen MINLONGESTTRYPPEPLEN
 minimum length of the longest tryptic peptide
--maxreads MAXREADS
 stop early if we hit this many reads
--minreadcount MINREADCOUNT
 minimum read count
--out OUT Output metapeptide database file
--outfasta OUTFASTA
 Output metapeptide fasta database file
--debug Enable debug logging