NAME

CLIPSeqTools::App::all - Run all clipseqtools analyses

SYNOPSIS

clipseqtools all [options/parameters]

DESCRIPTION

Run all clipseqtools analyses.

OPTIONS

  Input options for library.
    --driver <Str>         driver for database connection (eg. mysql,
                           SQLite).
    --database <Str>       database name or path to database file for file
                           based databases (eg. SQLite).
    --table <Str>          database table.
    --host <Str>           hostname for database connection.
    --user <Str>           username for database connection.
    --password <Str>       password for database connection.
    --records_class <Str>  type of records stored in database.
    --filter <Filter>      filter library. May be used multiple times.
                           Syntax: column_name="pattern"
                           e.g. keep reads with deletions AND not repeat
                                masked AND longer than 31
                                -filter deletion="def"
                                -filter rmsk="undef" .
                                -filter query_length=">31".
                           Operators: >, >=, <, <=, =, !=, def, undef

  Other input
    -gtf <Str>             GTF file with genes/transcripts. [Required]
    -rname_sizes <Str>     file with sizes for reference alignment sequences
                           (rnames). Must be tab delimited (chromosome\tsize)
                           with one line per rname. [Required]

  Output
    --o_prefix <Str>       output path prefix. Script will create and add
                           extension to path. [Default: ./]

  Other options.
    --allowed_dis <Int>    reads closer than this value are assembled in
                           clusters. Default: 0
    --plot                 call plotting script to create plots.
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message