Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
129 lines (85 sloc) 5.54 KB

Utilities

SplitMetadata

Splits metadata file into separate metadata files according to the set of values in specified column(s). Can be handly for implementing pipelines using VDJtools.

Command line usage

$VDJTOOLS SplitMetadata [options] metadata.txt output_dir

Parameters:

Shorthand Long name Argument Description
-c --columns string1,string2,... A comma separated list of column name(s) to split metadata by.

Tabular output

Output resulting metadata files to specified folder. Unique combinations of metadata entries in specified columns will be appended to names of corresponding metadata files, relative sample paths will be handled appropriately.


FilterMetadata

Filters metadata by evaluating expression over values in specified metadata columns, e.g.:

"__chain__=~/TR[AB]/"
"__chain__=='TRA'||__chain__=='TRB'"
"__chain__.contains('TRA')"
"!__condition__.startsWith('control')"

Both Java and Groovy syntax are supported, column names should be marked by double underscores before and after the name.

Command line usage

$VDJTOOLS FilterMetadata [options] metadata.txt output_dir output_suffix

Parameters:

Shorthand Long name Argument Description
-f --filter expression Filter expression, should be surrounded with quotation marks, metadata column names should be marked with __.

Tabular output

Filtered metadata table with corresponding suffix will be created in the specified folder, relative sample paths will be handled appropriately.


Convert

Converts datasets from an arbitrary supported format to :ref:`vdjtools_format`. You can also re-normalize your data - collapse clonotypes by V, D, J and CDR3 nucleotide sequence and re-compute clonotype frequencies - by using -S VDJtoolsRenorm option. This is useful if you want to groom manually converted data, or somewhy your clonotype frequencies do not sum to 1.

Command line usage

$VDJTOOLS Convert \
[options] [sample1.txt sample2.txt ... if -m is not specified] output_prefix

Parameters:

Shorthand Long name Argument Description
-S --software path Format to convert from, see the :ref:`supported_input` section
-m --metadata path Path to metadata file. See :ref:`common_params`
-c --compress   Compressed output for clonotype table. See :ref:`common_params`

Tabular output

Outputs converted samples to the path specified by output prefix and creates a corresponding metadata file. Will also append conv:[-S value] to ..filter.. metadata column.


RInstall

Prints the list of required R packages and installs dependencies into a local library (RPackages folder) which is placed in the parent folder of VDJtools jar. If this routine does not return with "PASSED" message, manual installation of packages that failed to deploy is required.

Command line usage

$VDJTOOLS RInstall
You can’t perform that action at this time.