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$ /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
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.
The text was updated successfully, but these errors were encountered:
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,
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:
The same applies to the other command line tools with a
-help
switch, e.g.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:
The text was updated successfully, but these errors were encountered: