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lib/App/Egaz/Command/lpcnam.pm  view on Meta::CPAN

        # options:
        #    -gapOut=gap.tab - Output gap sizes to file
        #    -type=XXX - Restrict output to particular type in net file
        #    -splitOnInsert - Split chain when get an insertion of another chain
        #    -wholeChains - Write entire chain references by net, don't split
        #     when a high-level net is encoundered.  This is useful when nets
        #     have been filtered.
        #    -skipMissing - skip chains that are not found instead of generating
        #     an error.  Useful if chains have been filtered.
        #
        # chainStitchId - Join chain fragments with the same chain ID into a single
        #    chain per ID.  Chain fragments must be from same original chain but
        #    must not overlap.  Chain fragment scores are summed.
        # usage:
        #    chainStitchId in.chain out.chain
        $cmd
            = "netChainSubset -verbose=0 $outdir/noClass.net"
            . " $outdir/all.chain"
            . " stdout"
            . " | chainStitchId"
            . " stdin"
            . " $outdir/over.chain";
        App::Egaz::Common::exec_cmd( $cmd, { verbose => $opt->{verbose}, } );

lib/App/Egaz/Command/template.pm  view on Meta::CPAN

            }
        ],
        [],
        [ "outdir|o=s",   "Output directory", { default => "." }, ],
        [ "queue=s",      "QUEUE_NAME",       { default => "mpi" }, ],
        [ "separate",     "separate each Target-Query groups", ],
        [ "tmp=s",        "user defined tempdir", ],
        [ "parallel|p=i", "number of threads", { default => 2 }, ],
        [ "verbose|v",    "verbose mode", ],
        [],
        [ "length=i",  "minimal length of alignment fragments", { default => 1000 }, ],
        [ "partition", "use partitioned sequences if available", ],
        [ "msa=s",     "aligning program for refine alignments", { default => "mafft" }, ],
        [ "taxon=s",   "taxon.csv for this project", ],
        [ "aligndb",   "create aligndb scripts", ],
        [],
        [ "multiname=s", "naming multiply alignment", ],
        [ "outgroup=s",  "the name of outgroup", ],
        [ "tree=s",      "a predefined guiding tree for multiz", ],
        [ "order",       "multiple alignments with original order (using fake_tree.nwk)", ],
        [ "fasttree", "use FastTree instead of RaxML to create a phylotree", ],