Template File Contents

This article describes the metadata, tokens, and special characters that you can include in your custom template files for use with the Template File Generator.

Available from: BaseSpace Clarity LIMS v5.1.x

Metadata

The following table lists and describes the metadata elements that you can include in your template files.

• Unless otherwise specified, metadata elements are optional. In some cases, a metadata element must be used in conjunction with another element. For example, ILLEGAL.CHARACTERS must be used with ILLEGAL.CHARACTER.REPLACEMENTS.

• Unless otherwise specified, metadata elements can appear multiple times in the template. However, if they are paired with values, only the first occurrence is used. The other lines are silently ignored.

• Unless otherwise specified, if a metadata element requires a single value, any additional values are ignored when the file is generated. For example, suppose you include the OUTPUT.TARGET.DIR <path> metadata in your template file and provide more than one value for <path>. The script will process only the first (valid) path value and will ignore all other values.

• Unless "metadata syntax must match exactly" is specified, metadata elements are detected and used even if there is text appended before or after them. For example the following expressions are equivalent:

  LIST.SEPARATOR, COMMA
  This-expression-is-equivalent-LIST.SEPARATOR-to-the-one-above, COMMA

For more information on metadata and how to use metadata elements in your template files, see Metadata in Creating Template Files article.

Metadata Element	Description	Examples
CONTROL.SAMPLE.DEFAULT.PROJECT.NAME, <project name>	Defines a project name for control samples. The value specified is used to determine the SAMPLE.PROJECT.NAME and SAMPLE.PROJECT.NAME.ALL token values. If not specified, the default project name for control samples is left empty. If no project name follows the metadata element, the project name is left empty.	CONTROL.SAMPLE.DEFAULT.PROJECT.NAME, My Control Sample Project See also Defining a project name for control samples.
EXCLUDE.CONTROL.TYPES, <control-type name>, <control-type name>, ...	Excludes control inputs that have a control-type uri matching an entry from the exclusion list. The metadata entry must be followed by one or more control-type name, otherwise file generation is aborted. Each control-type name must exist in the LIMS and the metadata syntax must match exactly. If this is not the case, file generation continues, but a warning message displays and a warning is logged in the log file. A warning is issued if the metadata element is included more than once.	EXCLUDE.CONTROL.TYPES, PhiX v3, EXCLUDE.CONTROL.TYPES, PhiX v3, Endogenous Positive Control
EXCLUDE.CONTROL.TYPES.ALL	Excludes all control types. Takes precedence over EXCLUDE.CONTROL.TYPES The metadata syntax must match exactly. If this metadata element is included more than once, file generation completes, but a warning message is logged in the log file.
EXCLUDE.INPUT.ANALYTES	Excludes inputs of type Analyte (derived sample) from the generated file. If used without the INCLUDE.INPUT.RESULTFILES element, the generated files will be empty. File generation finishes with a warning message and a warning is logged in the log file.
EXCLUDE.OUTPUT.ANALYTES	Excludes outputs of type Analyte (derived sample) from the generated file. The generated file(s) will be empty if: This element is used without the INCLUDE.OUTPUT.RESULTFILES element. There is no per input or shared result file output analyte in the step (or container if a GROUP.FILES.BY is enabled). In both scenarios, file generation finishes with a warning message and a warning is logged in the log file.
GROUP.FILES.BY.<grouping>, <zip file name> The following groupings are supported: GROUP.FILES.BY.INPUT.CONTAINERS - generates one file per input container GROUP.FILES.BY.OUTPUT.CONTAINERS- generates one file per output container	Creates a file for each instance of the specified grouping, i.e., one file per input or per output container. The script gathers all files together into one zip file so only one file placeholder is needed. The metadata may be followed by the name of the zip file that will contain the grouped files. Otherwise, the value set by the -destLIMSID script parameter is used for the file name. The following scenarios will abort file generation: Collisions between the file names. (See OUTPUT.FILE.NAME) Attempting to group files by both input and output container in the same template.	GROUP.FILES.BY.INPUT.CONTAINERS, MyInputContainerFile GROUP.FILES.BY.OUTPUT.CONTAINERs, MyOutputContainerFile See also Generating Multiple Files.
HIDE, <token>, <token>, ... IF <case> The following case is supported: NODATA: Line/Column is removed if the token has no value.	Removes lines from the HEADER_BLOCK section and columns from the HEADER and DATA sections when a <token> matches the <case>. All HIDE lines in the template are treated. There can be one or more <token> on a HIDE line. If there is no <token> between HIDE and IF, file generation is aborted. All tokens must be part of the supported tokens list. Unsupported tokens will abort the file generation. Otherwise, file generation is aborted.
ILLEGAL.CHARACTERS, <character>, <character>, ... ILLEGAL.CHARACTER.REPLACEMENTS, <replacement>, <replacement>, ... <character> supports Special Character Mapping	Specifies characters that must not appear in the generated file, and replaces them. Each <character> is replaced by the matching <replacement> element. Refer to Special Characters section below to determine if the illegal character must be specified using a keyword. If ILLEGAL.CHARACTERS or ILLEGAL.CHARACTER.REPLACEMENTS is missing, file generation completes with a warning message and a warning is logged in the log file. No character replacement is performed. The lists following ILLEGAL.CHARACTERS and ILLEGAL.CHARACTER.REPLACEMENTS must match 1-to-1 in order. Otherwise, file generation completes with a warning message and a warning is logged in the log file. No character replacement is performed.	ILLEGAL.CHARACTERS,PERIOD ILLEGAL.CHARACTER.REPLACEMENTS,_ ILLEGAL.CHARACTERS,TAB,PERIOD,#,<,> ILLEGAL.CHARACTER.REPLACEMENTS,,,_,","
INCLUDE.INPUT.RESULTFILES	Includes inputs of type ResultFile in the generated file. (By default these are excluded.) ℹ In LIMS v5 and later, ResultFile inputs are only supported in the API.
INCLUDE.OUTPUT.RESULTFILES	Includes outputs of type ResultFile in the generated file. (By default these are excluded.)
LIST.SEPARATOR, <separator> <separator> supports Special Character Mapping	Specifies character(s) used to separate elements for tokens that return lists (e.g., SAMPLE.PROJECT.NAME.ALL). If this metadata is not specified, COMMA is used by default. Must be followed by the separator character(s) to be used. If no separator is specified, file generation is aborted. Refer to the Special Characters section below to determine if the character must be provided using a keyword.	LIST.SEPARATOR,"; "
OUTPUT.FILE.NAME, <file name>	Specifies the name for the generated file(s). The metadata syntax must match exactly. A subset of tokens is supported in the file name. If the metadata element is not followed by the file name, file generation is aborted. If this metadata element is not provided or is incomplete, the value of the -o script parameter is used instead. This causes collisions when multiple files are generated. In this case, file generation completes with an exception message and a warning is logged in the log file. Using a path in the file name is deprecated, but still supported (update to OUTPUT.TARGET.DIR). File generation finishes with a warning message and a warning is logged in the log file. Characters in the file name must be either alpha-numeric, underscores, dashes or periods. Illegal characters are replaced (see OUTPUT.FILE.NAME.ILLEGAL.CHARACTER.REPLACEMENT) File generation finishes with a warning message and a warning is logged in the log file.	OUTPUT.FILE.NAME,NewTemplateFileName.csv You can include 'grouping' tokens in the file name, which allows you to create unique file names when generating multiple files. For details and a list of supported tokens, see Using Token Values in File Names.
OUTPUT.FILE.NAME.ILLEGAL.CHARACTER.REPLACEMENT, <replacement>	Specifies the character(s) to use when replacing illegal characters in file names. Legal characters are either alpha-numeric or an underscore, dash or period. If this metadata element is not present, an underscore is used instead. (File generation finishes with a warning message and a warning is logged in the log file.) If the replacement character is an illegal character itself, an underscore is used. Must be followed by the character(s) to use for replacing illegal characters in file names. Otherwise, file generation is aborted.
OUTPUT.SEPARATOR, <separator> <separator> supports Special Character Mapping	Specifies the character(s) used to separate columns in the output. If this metadata is not specified, COMMA is used by default. Must be followed by the separator character(s) to be used. If no separator is specified, file generation is aborted. Refer to the Special Characters section below to determine if the separator must be provided using a keyword	OUTPUT.SEPARATOR,TAB
OUTPUT.TARGET.DIR, <path>	Specifies the name for the generated file(s). The metadata syntax must match exactly. A subset of tokens is supported in the file name. If the metadata element is not followed by a path, file generation is aborted. If this metadata element is not provided or is incomplete, the value of OUTPUT.FILE.NAME is used instead. If OUTPUT.FILE.NAME contains a path, it is replaced by <path>.	OUTPUT.TARGET.DIR,/Users/LabTech/TemplateFiles/ See also Using Token Values in File Names.
PROCESS.POOLED.ARTIFACTS	Includes pools in the generated file as if they were regular input artifacts. When this metadata element is present, it uses demultiplexing logic and prints one row per sample in the pool. In the case of a submitted pool, sample names are generated following this pattern: “<pool-name>-<reagent-id>” If an input is not pooled in this mode, the input is treated as a pool of one sample. If the input is a pool of pools with only one sample, then it prints out as a pooled artifact instead of an input prior to the pool. If this metadata element is not included, if the input is a pool, it is treated as if it were a single sample and only one row is output in the file.
SCRIPT.VERSION, <major>.<minor>.<patch>	Provides the version of the compatible DriverFileGenerator.jar file. Version compatibility is only checked if this metadata is present. <major>.<minor>.<patch> must all be present. Otherwise, file generation is aborted. File generation is aborted if SCRIPT.VERSION <major> does not match the Template File Generator version. The file generation continues with a warning if the SCRIPT.VERSION is later than the Template File Generator version (<minor> and <patch> only). ⚠ Ensure your NGS version is up to date.	SCRIPT.VERSION,1.0.2
SORT.BY.${token}, ${token}, ...	Sorts the <DATA> rows based on the ${token} specified. There is no reverse order. If the SORT.BY. metadata element is not followed by ${token}, it is silently ignored.	SORT.BY.${INPUT.CONTAINER.ROW}${INPUT.CONTAINER.COLUMN} See Sorting Logic.
SORT.VERTICAL	Sorts the <DATA> rows based on container column placement. SORT.BY.${INPUT.CONTAINER.ROW}${INPUT.CONTAINER.COLUMN} must also be present in the template. Otherwise SORT.VERTICAL will have no effect and is silently ignored.	See Sorting Logic.

Tokens

A token is a placeholder variable that is replaced with unique data at run time. You can include tokens in automation command lines, in scripts, and in template files.

For example, suppose you include the INPUT.CONTAINER.NAME token in a template file generated by a step. At run time, this token is replaced with the name of the container that was input to the step.

All tokens included in a template file must appear in the following form: ${TOKEN}, for example - ${INPUT.CONTAINER.NAME}.

Input and Output Tokens

For steps with ResultFile inputs or outputs, refer to the following entries in the Metadata table:

• INCLUDE.INPUT.RESULTFILES

• INCLUDE.OUTPUT.RESULTFILES

Token	Description
INPUT.LIMSID OUTPUT.LIMSID	The LIMS ID of a given input / output
INPUT.NAME OUTPUT.NAME	The name of a given input / output
INPUT.CONTAINER.COLUMN OUTPUT.CONTAINER.COLUMN	The column part of the placement of a given input / output in its container
INPUT.CONTAINER.LIMSID OUTPUT.CONTAINER.LIMSID	The LIMS ID of the container of a given input / output Also supported in: HEADER_BLOCK file name
INPUT.CONTAINER.NAME OUTPUT.CONTAINER.NAME	The name of the container of a given input / output Also supported in: HEADER_BLOCK file name
INPUT.CONTAINER.PLACEMENT OUTPUT.CONTAINER.PLACEMENT	The placement of a given input / output in its container. Format defined in the <PLACEMENT> segment
INPUT.CONTAINER.ROW OUTPUT.CONTAINER.ROW	The row part of the placement of a given input / output in its container
INPUT.CONTAINER.TYPE OUTPUT.CONTAINER.TYPE	The type of container holding a given input / output Also supported in: HEADER_BLOCK file name
INPUT.CONTAINER.UDF.<udf name> OUTPUT.CONTAINER.UDF.<udf name>	Get the value of a UDF on the container of a given input / output
INPUT.REAGENT.CATEGORY OUTPUT.REAGENT.CATEGORY	List of categories of reagent on a given input / output
INPUT.REAGENT.NAME OUTPUT.REAGENT.NAME	List of reagents on an input / output
INPUT.REAGENT.SEQUENCE OUTPUT.REAGENT.SEQUENCE	List the sequence of each category of reagent on a given input / output
INPUT.UDF.<udf name> OUTPUT.UDF.<udf name>	Get the value of a UDF on a given input / output
INPUT.POOL.NAME	If the current input is a pool, provides its name. Empty if the input is not a pool
INPUT.POOL.PLACEMENT	If the current input is a pool, provides its placement (not affected by the <PLACEMENT> section) Empty if the input is not a pool.
INPUT.POOL.UDF.<udf name>	If the current input is a pool, provides one of its UDFs. Empty if the input is not a pool.

Process Tokens

Token	Description
PROCESS.LIMSID	The LIMS ID of the current process Also supported in: HEADER_BLOCK file name
PROCESS.NAME	The name of the current process
PROCESS.UDF.<udf name>	Get the value of a process UDF (on the current step) Also supported in: HEADER_BLOCK file name
PROCESS.TECHNICIAN See Upgrade Note in Creating Template Files article.	The first and last name of the technician running the current process. Also supported in: HEADER_BLOCK file name

Submitted Sample Tokens

Token	Description
SAMPLE.LIMSID	List of all submitted sample LIMS IDs of a given artifact
SAMPLE.NAME	List of all submitted sample names of a given artifact
SAMPLE.UDF.<udf name>	Get the value of a UDF for the project containing the submitted samples of a given artifact
SAMPLE.UDT.<udt name>.<udf name>	Get the value of a UDT UDF on the submitted samples of a given artifact
SAMPLE.PROJECT.CONTACT	List of the project contacts for all submitted samples of a given artifact
SAMPLE.PROJECT.CONTACT.ALL	List of the project contacts for the submitted samples of all artifacts. Prints all unique project contact names in a line (first name followed by last name) separated by LIST.SEPARATOR. Also supported in: HEADER_BLOCK file name
SAMPLE.PROJECT.LIMSID	List of the project LIMS IDs for all submitted samples of a given artifact
SAMPLE.PROJECT.NAME	List of projects for all submitted samples of a given artifact (uses CONTROL.SAMPLE.DEFAULT.PROJECT.NAME)
SAMPLE.PROJECT.NAME.ALL	List of projects for the submitted samples of all artifacts (uses CONTROL.SAMPLE.DEFAULT.PROJECT.NAME). Prints all unique project names in a line, separated by LIST.SEPARATOR. Also supported in: HEADER_BLOCK file name
SAMPLE.PROJECT.UDF.<udf name>	Get the value of a UDF for the project containing the submitted samples of a given artifact. Example: ${SAMPLE.PROJECT.UDF.My Project Level Field}

Other Tokens

Token	Description
DATE	Current date (i.e., when the script is run). The default format uses the host's locale setting.
INDEX	Row number of the data row (in <DATA> segment), starting from 1

Special Characters

CSV and template file generation special characters have substitution symbols within templates.

Substitution Symbol	Character Represented
ASTERISK	*
BACKSLASH	\
CARET	^
CLOSING_BRACE	}
CLOSING_BRACKET	]
CLOSING_PARENTHESIS	)
COMMA	,
DOLLAR_SIGN	$
DOUBLE_QUOTE	"
OPENING_BRACE	{
OPENING_BRACKET	[
OPENING_PARENTHESIS	(
PERIOD	.
PIPE	|
PLUS_SIGN	+
QUESTION_MARK	?
SINGLE_QUOTE	'
TAB	tab