Improve command line help text with tool descriptions

[peterjc]

There is a lot of useful information on http://flapjack.hutton.ac.uk/en/latest/command_line_support.html which could be included within the command line help itself.

e.g. Under macOS using Flapjack v1.18.06.29,

$ /Applications/Flapjack.app/Contents/Resources/app/cmd/mabcstats -help
usage: GenerateMabcStats -d <INTEGER> -g <FILE> -m <FILE> -o <FILEPATH> -q
       <FILE> -r <INTEGER> [-A] [-C] [-c <FLOATING POINT NUMBER>] [-D]
       [-E] [-M <arg>] [--model <ARG>] [-p <FILE>] [-S <arg>] [-T] [-t
       <FILE>] [-x]
 -d,--donor-parent <INTEGER>                        Index of parent in
                                                    file
 -g,--genotypes <FILE>                              Genotype file
 -m,--map <FILE>                                    Map file
 -o,--output <FILEPATH>                             Desired output
                                                    filepath
 -q,--qtls <FILE>                                   QTL file
 -r,--recurrent-parent <INTEGER>                    Index of parent in
                                                    file
 -A,--all-chromosomes                               Duplicate all markers
                                                    onto a single All
                                                    Chromosomes chromosome
                                                    for side-by-side
                                                    viewing
 -C,--collapse-heteozygotes                         Don't distinguish
                                                    between heterozygous
                                                    alleles (eg treat A/T
                                                    the same as T/A)
 -c,--max-marker-coverage <FLOATING POINT NUMBER>   Maximum coverage a
                                                    marker can have in the
                                                    weighted model
 -D,--allow-duplicates                              Allow duplicate line
                                                    names
 -E,--decimal-english                               Optional input
                                                    parameter
 -M,--missing-data <arg>                            The string used to
                                                    represent missing data
                                                    (default is "-" or use
                                                    "" for empty string)
    --model <ARG>                                   weighted|unweighted
 -p,--project <FILE>                                Project file
 -S,--heterozygous-separator <arg>                  The string used to
                                                    separate heterozygous
                                                    alleles (default is
                                                    "/" or use "" for no
                                                    separator)
 -T,--transposed                                    Genotype data is
                                                    transposed compared to
                                                    Flapjack's default
 -t,--traits <FILE>                                 Trait file
 -x,--exclude-additional-parents                    Exclude parents which
                                                    are not the selected
                                                    recurrent, or donor,
                                                    parent from the
                                                    analysis

Quoting from http://flapjack.hutton.ac.uk/en/latest/command_line_support.html it would be helpful to include this as the usage text at the start of the command line help:

This program will take input data files and run Flapjack’s Marker Assisted Back Crossing statistics module upon them, outputting a tab-delimited text file with results similar to those shown directly in Flapjack’s table view had the UI been used.

The same applies to the other command line tools with a -help switch, e.g.

$ /Applications/Flapjack.app/Contents/Resources/app/cmd/splitproject -help
Flapjack null

Splits a Flapjack project into multiple raw data text files.

SPLITPROJECT -PROJECT=project -DIR=dir
             [-DATASETIN=datasetin [-DATASETOUT=datasetout]]
             [-DECIMALENGLISH]

  project           The location of the project to process.
  dir               The location to write the output files to.
  datasetin         Specifies the name of a dataset within the project file
                    to process. If no names are specified, then all datasets
                    will be extracted.
  datasetout        Overrides the given datasetin name with a new name to use
                    when outputting that dataset's files.
  decimalEnglish    Specifies that all numbers will be processed using the
                    English decimal mark separator (dot rather than a comma).

Note that dataset names in Flapjack are case sensitive.
You can process multiple datasets at once, eg:
  -DATASETIN dsin1 -DATASETOUT dsout1 -DATASETIN dsin2 -DATASETOUT dsout2

The "null" on the first line is odd, but at least it does say "Splits a Flapjack project into multiple raw data text files." - but it would benefit from adding this from the website help:

This program can be used to take a genotype file containing a set of lines, and will generate a (new) expected F1 line by combining the alleles of two selected parental lines.