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.

Metadata

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

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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.

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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.

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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.

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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 the Creating Template Files article > Metadata section.

Metadata Element

Description

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.

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If not specified, the default project name for control samples is left empty.

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If no project name follows the metadata element, the project name is left empty.

Examples:

CONTROL.SAMPLE.DEFAULT.PROJECT.NAME, My Control Sample Project

See also Creating Template Files article > Examples section > 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.

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The metadata entry must be followed by one or more control-type name, otherwise file generation is aborted.

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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.

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A warning is issued if the metadata element is included more than once.

Examples:

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

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The metadata syntax must match exactly.

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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:

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This element is used without the INCLUDE.OUTPUT.RESULTFILES element.

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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:

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GROUP.FILES.BY.INPUT.CONTAINERS- generates one file per input container

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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:

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Collisions between the file names. (See OUTPUT.FILE.NAME)

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Attempting to group files by both input and output container in the same template.

Examples:

GROUP.FILES.BY.INPUT.CONTAINERS, MyInputContainerFile

GROUP.FILES.BY.OUTPUT.CONTAINERs, MyOutputContainerFile

See also Creating Template Files article > Examples section > Generating multiple files.

HIDE, <token>, <token>, ... IF <case>

The following case is supported:

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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>.

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All HIDE lines in the template are treated.

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There can be one or more <token> on a HIDE line.

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If there is no <token> between HIDE and IF, file generation is aborted.

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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.

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Each <character> is replaced by the matching <replacement> element.

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Refer to Special characters section below to determine if the illegal character must be specified using a keyword.

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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.

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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.

Examples:

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.)

Note:

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In LIMS v4.2, ResultFile inputs are only supported in the Operations Interface and API.

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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).

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If this metadata is not specified, COMMA is used by default.

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Must be followed by the separator character(s) to be used. If no separator is specified, file generation is aborted.

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Refer to the Special characters section below to determine if the character must be provided using a keyword

Example:

LIST.SEPARATOR,"; "

OUTPUT.FILE.NAME, <file name>

Specifies the name for the generated file(s).

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The metadata syntax must match exactly.

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A subset of tokens is supported in the file name.

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If the metadata element is not followed by the file name, file generation is aborted.

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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 (See Script parameters > Output file). In this case, file generation completes with an exception message and a warning is logged in the log file.

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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.

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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)

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File generation finishes with a warning message and a warning is logged in the log file.

Examples:

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 Creating Template Files article > Examples section > 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.

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Legal characters are either alpha-numeric or an underscore, dash or period.

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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. )

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If the replacement character is an illegal character itself, an underscore is used.

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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.

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If this metadata is not specified, COMMA is used by default.

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Must be followed by the separator character(s) to be used. If no separator is specified, file generation is aborted.

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Refer to the Special characters section below to determine if the separator must be provided using a keyword

Example:

OUTPUT.SEPARATOR,TAB

OUTPUT.TARGET.DIR, <path>

Specifies the name for the generated file(s).

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The metadata syntax must match exactly.

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A subset of tokens is supported in the file name.

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If the metadata element is not followed by a path, file generation is aborted.

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If this metadata element is not provided or is incomplete, the value of OUTPUT.FILE.NAME is used instead.

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If OUTPUT.FILE.NAME contains a path, it is replaced by <path>.

Example:

OUTPUT.TARGET.DIR,/Users/LabTech/TemplateFiles/

See also Creating Template Files article > Examples section > Using token values in file names.

PROCESS.POOLED.ARTIFACTS

Includes pools in the generated file as if they were regular input artifacts.

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When this metadata element is present, it uses demultiplexing logic and prints one row per sample in the pool.

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In the case of a submitted pool, sample names are generated following this pattern: “<pool-name>-<reagent-id>”

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If an input is not pooled in this mode, the input is treated as a pool of one sample.

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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.

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Version compatibility is only checked if this metadata is present.

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<major>.<minor>.<patch> must all be present. Otherwise, file generation is aborted.

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File generation is aborted if SCRIPT.VERSION <major> does not match the Template File Generator version.

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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.

Example:

SCRIPT.VERSION,1.0.2

SORT.BY.${token}, ${token}, ...

Sorts the <DATA> rows based on the ${token} specified.

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There is no reverse order.

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If the SORT.BY. metadata element is not followed by ${token}, it is silently ignored.

Example:

SORT.BY.${INPUT.CONTAINER.ROW}${INPUT.CONTAINER.COLUMN}

See C reating Custom Template Files article > Sorting logic section.

SORT.VERTICAL

Sorts the <DATA> rows based on container column placement.

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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.

Example:

See C reating Custom Template Files article > Sorting logic section.

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:

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INCLUDE.INPUT.RESULTFILES

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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:

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HEADER_BLOCK

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file name

INPUT.CONTAINER.NAME

OUTPUT.CONTAINER.NAME

The name of the container of a given input / output

Also supported in:

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HEADER_BLOCK

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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:

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HEADER_BLOCK

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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:

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HEADER_BLOCK

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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:

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HEADER_BLOCK

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file name

PROCESS.TECHNICIANSee Upgrade note in Creating Template Files article.

The first and last name of the technician running the current process

Also supported in:

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HEADER_BLOCK

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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:

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HEADER_BLOCK

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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:

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HEADER_BLOCK

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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