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