Creating Sample Input Sheet Templates

Compatibility—NGS v5.16 and earlier

New in NGS 5.4—Input and output container UDF tokens

Before creating a sample input sheet template, ensure that you understand the sections of the template - as described in Sample Input Sheet Template Sections

The sample input sheet template is a comma-delimited CSV file. Its format must follow a few basic rules:

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Metadata entries must each appear on a new line and be the only entry on that line. Metadata entries must not appear inside tags.

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Opening and closing tags must appear exactly as they are outlined below, on a new line and as the only entry on that line.

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Each opened tag must be closed, otherwise it is skipped by the script.

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The order of tags must be preserved: <HEADER_BLOCK>, <HEADER>, <DATA>, <FOOTER>

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Any sections (opening tag + closing tag combination) can be omitted from the template file.

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Entries that are separated by commas in the template will be delimited by the metadata-specified separator (default: COMMA) in the sample input sheet.

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White space is allowed in the template. However, if there is a blank line inside a tag, it will also be present in the sample input sheet produced.

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If an entry in the template is enclosed in double quotes it will be imported as a single entry and written to the sample input sheet as such, even if it has commas inside.

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To include double-quotes (or single-quotes) in the sample input sheet, use theescape character: Example: \" or \'

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To include an escape character in the sample input sheet, use two escape characters inside double-quotes. For example if you want to see \\Share\Folder\Filename.txt use "\\\\Share\\Folder\\Filename.txt" as the token.

Tokens

All of the tokens below must appear in the template in the following form: ${TOKEN}.

Example: ${PROCESS.LIMSID}

If your process contains ResultFile inputs or outputs, please refer to the Metadata section, specifically INCLUDE.INPUT.RESULTFILES and INCLUDE.OUTPUT.RESULTFILES.

Input and OutputTokens

Input Tokens	Output Tokens
INPUT.LIMSID	OUTPUT.LIMSID
INPUT.NAME	OUTPUT.NAME
INPUT.CONTAINER.NAME	OUTPUT.CONTAINER.NAME
INPUT.CONTAINER.LIMSID	OUTPUT.CONTAINER.LIMSID
INPUT.CONTAINER.TYPE	OUTPUT.CONTAINER.TYPE
INPUT.CONTAINER.ROW	OUTPUT.CONTAINER.ROW
INPUT.CONTAINER.COLUMN	OUTPUT.CONTAINER.COLUMN
INPUT.CONTAINER.PLACEMENT	OUTPUT.CONTAINER.PLACEMENT
INPUT.CONTAINER.UDF.name	OUTPUT.CONTAINER.UDF.name
INPUT.UDF.<UDF NAME>	OUTPUT.UDF. <UDF NAME>
INPUT.REAGENT.NAME	OUTPUT.REAGENT.NAME
INPUT.REAGENT.CATEGORY	OUTPUT.REAGENT.CATEGORY
INPUT.REAGENT.SEQUENCE	OUTPUT.REAGENT.SEQUENCE
INPUT.POOL.NAME
INPUT.POOL.PLACEMENT
INPUT.POOL.UDF. <UDF NAME>

Process Tokens

Process Tokens	Submitted Sample Tokens
PROCESS.LIMSID	SAMPLE.LIMSID
PROCESS.NAME	SAMPLE.NAME
PROCESS.TECHNICIAN	SAMPLE.PROJECT.CONTACT
PROCESS.UDF.<UDF NAME>	SAMPLE.UDF. <UDF NAME>
	SAMPLE.PROJECT.NAME
	SAMPLE.PROJECT.LIMSID
	SAMPLE.UDT. <UDT NAME> . <UDF NAME>

Misc Tokens

Misc Tokens	Description
INDEX	Row number of the data row, index starting from 1
DATE	Current date (i.e., when the script is being run)
SAMPLE.PROJECT.NAME.ALL	Prints all unique project names in a line, separated by LIST.SEPARATOR
SAMPLE.PROJECT.CONTACT.ALL	Prints all unique project contact names in a line (first name followed by last name) separated by LIST.SEPARATOR

Metadata

Each metadata entry must be on a separate line. These are not data tokens, so they do not need to be enclosed in tags.

When using OUTPUT.FILE.NAME, you may wish to give the file a name that does not begin with the LIMSID of the placeholder it will be attached to in the LIMS. To still attach this file, the quickAttach and destLIMSID parameters may be used in the EPP configuration for the sample input sheet file generation.

Name of Metadata Entry	Description
SCRIPT.VERSION	Version of the compatible DriverFileGenerator.jar file, please include this entry into your templates. Example: SCRIPT.VERSION,1.0.2
OUTPUT.TARGET.DIR	Provide this token to specify the directory in which to write the sample input sheet file . If the directory or its parent directories do not exist, they will be created. Example: OUTPUT.TARGET.DIR,/Users/LabTech/DriverFiles/
OUTPUT.FILE.NAME	Provide this token to rename the sample input sheet with the specified name. Example: OUTPUT.FILE.NAME,NewDriverFileName.csv
OUTPUT.SEPARATOR	The sample input sheet will be delimited with the specified separator. The default sample input sheet delimiter used is COMMA. Refer to the Special Characters section of this page to determine if the separator must be provided using a keyword. Example: OUTPUT.SEPARATOR,TAB
LIST.SEPARATOR	Tokens that return lists (e.g., SAMPLE.PROJECT.NAME.ALL) will be separated by the specified String. Example: LIST.SEPARATOR,"; "
ILLEGAL.CHARACTERS	Specify characters that must not appear in the file produced. Each illegal character will be replaced with its corresponding replacement specified by the replacements token. Refer to the Special Characters section of this page to determine if the illegal character must be specified using a keyword. Example: ILLEGAL.CHARACTERS,TAB,PERIOD,#,<,>,etc
ILLEGAL.CHARACTER.REPLACEMENTS	Provides the replacement policy for each illegal character. The number of replacements provided must match the number of specified illegal characters (If only one replacement character is specified, it will be used to replace all illegal characters); replacement will be performed in corresponding order. Example: ILLEGAL.CHARACTER.REPLACEMENTS, _,",",_,_ ,_,_ ILLEGAL.CHARACTER.REPLACEMENTS,_
SORT.BY.	Specify tokens by which the data will be sorted alphanumerically within the sample input sheet file. More than one token can be provided e.g., to sort by container placement by row follow the usage example to the right, to sort by placement with multiple containers present provide the container name token as a sort option as well. For more information, see Sorting Logic. Example: SORT.BY.${INPUT.CONTAINER.ROW}${INPUT.CONTAINER.COLUMN}
SORT.VERTICAL	Sort data by container placement by column. SORT.BY.${INPUT.CONTAINER.ROW}${INPUT.CONTAINER.COLUMN} must be present in the template as well, otherwise SORT.VERTICAL will have no effect. For more information, see Sorting Logic. Example: SORT.VERTICAL
PROCESS.POOLED.ARTIFACTS	Include artifacts stored in pools into the sample input sheet generation as if they were regular input artifacts. Example: PROCESS.POOLED.ARTIFACTS
INCLUDE.INPUT.RESULTFILES	Includes input ResultFiles in the sample input sheet file. (By default these are excluded.) Example: INCLUDE.INPUT.RESULTFILES
INCLUDE.OUTPUT.RESULTFILES	Includes output ResultFiles in the sample input sheet file. (By default these are excluded.) Example: INCLUDE.OUTPUT.RESULTFILES
EXCLUDE.INPUT.ANALYTES	Excludes analyte (sample) inputs from the sample input sheet file. (By default these are included.) Example: EXCLUDE.INPUT.ANALYTES
EXCLUDE.OUTPUT.ANALYTES	Excludes analyte ( sample) outputs from the sample input sheet file. (By default these are included.) Example: EXCLUDE.OUTPUT.ANALYTE

Special Characters

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