Command line parameters

It is possible to specify command line parameters for automating certain functions. If not specified otherwise, clarity.exe file can be run with the same or different set of parameters again and again. This creates new instance, which is temporary and just passes new parameters into Clarity station that is already running.

Some of the command line parameters may be also defined in the others.ini file (by default located in C:\Clarity\Cfg). Used settings will override any of the same parameters used in the command line. Others.inifile supports the use of following command line parameters: bad_trace_cnt, create_emf_during_pdf, dump_memory, enable_asserts, mail_dump, report_cmdline_in_bad_trace.

All command line parameters are processed in the order they are set on the command line. It is thus usually necessary to open the file first, before making any changes to it (for example, open calibration, open chromatogram, recalibrate the calibration on the given level, close chromatogram and close calibration, in this order).

Each use of command line for controlling Clarity is recorded in Audit Trail including all parameters called.

No wildcards (*, ?) are allowed in the command line.

All parameters (but not file paths etc.) are case-sensitive, unless stated otherwise. No spaces are allowed between the command and the argument and in the argument itself.

Example: clarity.exe command=value is correct while clarity.exe command = value is wrong.

If you want to use spaces or other white space in parameters, you may use the quotation marks to do so.

Example: clarity.exe c=“C:\Documents and Settings\Smith\Desktop\Ethanol in blood.met” or clarity.exe user=“John Doe”.

See additional examples bellow the list of commands.

List of commands

 

abort
description:

Stops the single analysis/sequence measurement on the specified Instrument. This parameter is suitable for automatic testing. Does the same as stop command line parameter, but it does not store the chromatogram measured up to the time of abort.
syntax:

abort=VALUE

possible values:

1 (for Instrument 1), 2 (for Instrument 2), 4 (for Instrument 3), 8 (for Instrument 4), and their binary combinations.
implicit value:

None.
example:

clarity.exe abort=7 (will abort single analysis/sequence on Instruments 1, 2 and 3)
bad_trace_cnt
description:

Sets the number of lines in the BadTrace.txt file. Maximum value is 10 000 (exceeding value will be converted to 10 000). This parameter may be also used (and is overwritten by settings) in DataApex.ini file.
syntax:

bad_trace_cnt=VALUE

possible values:

0 - virtually any number
implicit value:

100
example:

clarity.exe bad_trace_cnt=1000

cal_apply
description:

Applies the specified calibration to the active chromatogram. It is recommended to use absolute paths because the calibration file will not be searched for in the working directory but in the calibration directory of the active project.
syntax:

cal_apply=PATH\FILENAME

possible values:

A valid path to the calibration (*.cal) file.
implicit value:

None.
example:

clarity.exe cal_apply=C:\CLARITY\DataFiles\WORK1\Calib\1.cal

cal_save
description:

Saves the active calibration. Use together with the instrument parameter to specify the Instrument whose Calibration window holds the calibration file you are interested in. Calibration file can be opened by specifying its path and filename. It is recommended to use absolute paths.

This command is ignored in GPC mode - use gal_save instead.

syntax:

cal_save

possible values:

None.
implicit value:

None.
example:

clarity.exe i=2 cal_save - saves the calibration opened in the second Instrument.
cal_save_as
description:

Saves the active calibration under the specified name. Use together with the instrument parameter to specify the Instrument whose Calibration window holds the calibration file you are interested in. Calibration file can be opened by specifying its path and filename. It is recommended to use absolute paths.

This command is ignored in GPC mode - use gal_save_as instead.

syntax:

cal_save_as=PATH\FILENAME

possible values:

A valid path to the calibration (*.cal) file.
implicit value:

None.
example:

clarity.exe cal_save_as=C:\CLARITY\DataFiles\WORK1\Calib\results.cal

cal_type
description:

Changes the type of calibration calculation for the active chromatogram. The parameter allows to specify calibration type for each signal of the chromatogram -the first character is corresponding to the first signal, second character to the second signal and so on.
syntax:

cal_type=TYPE

possible values:

any combination of _, U, I, E, N and S. For each signal in the chromatogram, a separate symbol is needed.

Characters used mean:

_ (underline) - do not change

U - uncalibrated

I - ISTD

E - ESTD

N - NORM

S - STDADD
implicit value:

_ (underline) for each signal.
example:

clarity.exe cal_type=_UIE (the first signal is left unchanged, the second is set to UNCAL, the third to ISTD, the fourth to ESTD).
cfg or g
description:

Opens the Clarity with the specified *.cfg file. Must be used when opening Clarity for the first time, otherwise it is ignored. Uses just the selected configuration file, not other files present in the \Cfg subdirectory.
syntax:

g=PATH\FILENAME

possible values:

The path to *.cfg file.
implicit value:

Empty.

If the path is not specified, the system will look for the *.cfg file in the \Cfg directory. If not found, the system will use the default Clarity.cfg file from the \Cfg directory.

When the path is specified absolutely, the Clarity will start with the *.cfg file specified.

When the path is specified relatively, the *.cfg file will be searched for in the directory relative to the current directory. Working directory will then be set to the new location.
example:

clarity.exe g=C:\CLARITY\Cfg\user1.cfg

clear_cal
description:

Clears the responses in the opened calibration file. When used with recal_level, the calibration is cleared first and recalibrated after that.
syntax:

clear_cal

possible values:

None.
implicit value:

None.
example:

clarity.exe test.cal clear_cal

control_devel_folder
description:

Adds additional path to be scanned for control module *.dll files. Can be used only once with one path, the path must be absolute. If both CLARITY\Bin and folder specified by using the control_devel_folder contain *.dll files with the same name or the same GUID, then only the file from control_devel_folder will be loaded. This parameter may be also used (and is overwritten by settings) in DataApex.ini file. Note that any control module loaded from the folder specified by using the control_devel_folder parameter will be considered unauthorized.
syntax:

control_devel_folder=PATH

possible values:

Absolute folder path.
implicit value:

None.
example:

clarity.exe control_devel_folder=C:\Dev\CTRL_Dlls\

create_emf_during_pdf
description:

Forces the creation of the *.emf file from which the *.pdf files are converted. This parameter may be also used (and is overwritten by settings) in DataApex.ini file.
syntax:

create_emf_during_pdf

possible values:

None.
implicit value:

None.
example:

clarity.exe create_emf_during_pdf

delayed_exit
description:

Exits Clarity after the time specified in seconds if it has no running acquisition and no running background threads (export, printing). This parameter is suitable for automatic testing.
syntax:

delayed_exit=VALUE

possible values:

Numeric.
implicit value:

None.
example:

clarity.exe delayed_exit=120

disable_message_boxes
description:

Suppresses the showing of message boxes. If Clarity would trigger a message box with a Yes-No-Cancel option then the preselected option will be applied. The Yes-No-Cancel dialog itself will not be shown but the option chosen is recorded to Audit Trail. Must be used when opening Clarity for the first time, otherwise it is ignored. This parameter is suitable for automatic testing.
syntax:

disable_message_boxes

possible values:

None.
implicit value:

None.
example:

clarity.exe disable_message_boxes

disable_send_report
description:

Suppresses the sending of error reports. If Clarity would trigger a message box with a Yes-No-Cancel option then the preselected option will be applied. The Yes-No-Cancel dialog itself will not be shown but the option chosen is recorded to Audit Trail. Must be used when opening Clarity for the first time, otherwise it is ignored. This parameter is suitable for automatic testing.
syntax:

disable_send_report

possible values:

None.
implicit value:

None.
example:

clarity.exe disable_send_report

dsk or k
description:

Opens the specified Instrument of Clarity with the specified desktop (*.dsk) file. Must be used when opening Clarity for the first time, otherwise it is ignored, the same command line must contain the number of the Instrument to be opened.
syntax:

k=PATH\FILENAME

possible values:

The path and filename of the *.dsk file.
implicit value:

Empty.

If the path is not specified, the system will look for the *.dsk file in the \Cfg directory. If not found, the system will use the default Clarity.dsk file from the \Cfg directory.
example:

clarity.exe k=C:\CLARITY\Cfg\Peter.dsk i=1

dump_memory
description:

Controls whether memory dump will be included in the crash dump (*.dmp file) in case Clarity crashes. Presence of the memory dump influences the size of the crash dump - with memory dump the dump file is about 200MB in size, without memory dump the crash dumps are about 1MB. This function can also be set via the DataApex.ini file that may be stored in Windows directory. Must be used when opening Clarity for the first time, otherwise it is ignored. dump_memory command line parameter has no effect if dump files are disabled by certain values of enable_asserts. This parameter is suitable for troubleshooting.
syntax:

dump_memory

possible values:

None.
implicit value:

None.
example:

clarity.exe dump_memory

enable_asserts
description:

Specifies what to do if an ASSERT (software developer check point) emerges. Must be used when opening Clarity for the first time, otherwise it is ignored. This parameter is suitable for troubleshooting, because it can make Clarity to create a process dump file that can be used in Debbuging tools for Windows to solve the problem. This parameter may also be used in DataApex.ini file (though the value will get overwritten if also specified on the command line).
syntax:

enable_asserts=VALUE

possible values:

0, 1, 2, .., 7

The meaning of particular values when ASSERT emerges are:

0 - Obsolete, same as 1.

1 - note is written into BadTrace.txt.

2 - note is written into BadTrace.txt and process dump file is created. The message box to send report is not displayed.

3 - note is written into BadTrace.txt and process dump file is created. The message box to send report is displayed. Recommended for testing and troubleshooting.

4 - Obsolete, same as 3.

5 - Obsolete, same as 1.

6 - Obsolete, same as 1.

7 - Obsolete, same as 3.
implicit value:

1 when enable_asserts command is omitted in the command line, 1 when enable_asserts command is used without a value.
example:

clarity.exe enable_asserts=3

err
description:

Stores the audit trail records also in the specified text file. File name is valid until it is replaced by a new one.
syntax:

err=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe err="C:\Users\<user name>\AppData\Local\Temp\CLARITY\error.txt"

exit
description:

Immediately exits Clarity. Does not work if acquisition is running or if any modal window is opened. This parameter is suitable for automatic testing.
syntax:

exit

possible values:

None.
implicit value:

None.
example:

clarity.exe exit

export_emf
description:

Exports the currently opened chromatograms into enhanced Windows metafile.
syntax:

export_emf=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe export_emf=C:\CLARITY\DataFiles\WORK1\Data\test.emf

export_results
description:

Exports the results of active chromatogram into the specified *.txt file and/or Clipboard (for more details see also chapter Export Data). Setting of the export is taken from the active *.cfg or *.dsk file.
syntax:

export_results=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe export_results="C:\Users\<user name>\AppData\Local\Temp\CLARITY\results.txt"

export_results_dbf
description:

Exports results of active chromatogram into specified database (*.dbf) file (for more details see also chapter Export Data). Setting of the export is taken from the active *.cfg or *.dsk file.
syntax:

export_results_dbf=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe export_results_dbf="C:\Users\<user name>\AppData\Local\Temp\CLARITY\results.dbf"

export_run_time
description:

Exports the Autostop Run Time value from the method currently opened on the Instrument as ANSI text into the specified file. Decimal separator is always ".". Exports "-1" when Autostop function is not enabled. In case of any error the text "No current method." is exported instead.
syntax:

export_run_time=PATH\FILENAME

possible values:

Any valid file name, including the path.
implicit value:

None.
example:

clarity.exe export_run_time="C:\Users\<user name>\AppData\Local\Temp\CLARITY\runtime.txt"

gal_apply
description:

Applies the specified GPC calibration to the active chromatogram. It is recommended to use absolute paths because the calibration file will not be searched for in the working directory but in the calibration directory of the active project.
syntax:

gal_apply=PATH\FILENAME

possible values:

A valid path to the GPC calibration (*.gal) file.
implicit value:

None.
example:

clarity.exe gal_apply="C:\Users\<user name>\AppData\Local\Temp\CLARITY\1.gal"

gal_save
description:

Saves the active GPC calibration. Use together with the instrument parameter to specify the Instrument whose Calibration window holds the GPC calibration file you are interested in. GPC calibration file can be opened by specifying its path and filename. It is recommended to use absolute paths.

This command is ignored when not in the GPC mode - use cal_save instead.
syntax:

gal_save

possible values:

None.
implicit value:

None.
example:

clarity.exe i=2 gal_save saves the calibration opened in the second Instrument.
gal_save_as
description:

Saves the active GPC calibration under the specified name. Use together with the instrument parameter to specify the Instrument whose Calibration window holds the GPC calibration file you are interested in. GPC calibration file can be opened by specifying its path and filename. It is recommended to use absolute paths.

This command is ignored when not in the GPC mode - use cal_save_as instead.
syntax:

gal_save_as=PATH\FILENAME

possible values:

A valid path to the calibration (*.gal) file.
implicit value:

None.
example:

clarity.exe gal_save_as="C:\Users\<user name>\AppData\Local\Temp\CLARITY\results.gal"

gpc
description:

Switches the Instrument into the GPC or Standard mode.
syntax:

gpc=VALUE

possible values:

0 or 1.
implicit value:

None.
example:

clarity.exe gpc=0

gpc_recal_stdno
description:

Together with the gpc_recal_type parameter enables to recalibrate an opened GPC calibration. The calibration is recalibrated by the active chromatogram at specified standard number and standard type. For successful recalibration it is necessary to specify the calibration file in the same command line as gpc_recal_stdno and gpc_recal_type parameters, which has to be both set to nonzero value.
syntax:

gpc_recal_stdno=VALUE

possible values:

0, 1, .. 20, 21 (Blank). Value 0 does nothing.
implicit value:

0
example:

clarity.exe test.gal gpc_recal_stdno=5 gpc_recal_type=1

gpc_recal_type
description:

Together with the gpc_recal_stdno parameter enables to recalibrate an opened GPC calibration. The calibration is recalibrated by the active chromatogram at specified standard number and standard type. For successful recalibration it is necessary to specify the calibration file in the same command line as gpc_recal_stdno and gpc_recal_type parameters, which has to be both set to nonzero value.
syntax:

gpc_recal_type=VALUE

possible values:

0, 1, 2.

The meaning of values are as follows:

0 - does nothing (no recalibration).

1 - narrow calibration type.

2 - broad calibration type.
implicit value:

0
example:

clarity.exe test.gal gpc_recal_stdno=5 gpc_recal_type=1

hide_splash
description:

Suppresses the splash screen that emerges when starting Clarity.
syntax:

hide_splash

possible values:

None.
implicit value:

None.
example:

clarity.exe hide_splash

instrument or i
description:

Automatically opens an Instrument specified by the number. The command line parameter for user (and password) should follow, otherwise the opening is stopped on the Login dialog.

Alternatively, it can be used as an accompanying parameter for specifying the number of the Instrument to perform other actions on, e.g., to define the Instrument on which a sequence should be imported using the seq_import parameter.
syntax:

i=VALUE

possible values:

1, 2, 3, 4. To open multiple Instruments, the clarity.exe file has to be called separately for each Instrument.
implicit value:

1
example:

clarity.exe i=3

To work with two or more Instruments at once, you should use the MS Batch "START" command. Examples section below the commands for more information.
mail_dump
description:

Disables the sending of memory dumps via e-mail. Must be used when opening Clarity for the first time, otherwise it is ignored. This parameter is suitable for troubleshooting, when users certainly do not want to mail 200MB files. This parameter may be also used (and is overwritten by settings) in DataApex.ini file.
syntax:

mail_dump=VALUE

possible values:

0 or 1.
implicit value:

1.
example:

clarity.exe mail_dump=0

met_apply
description:

Applies the specified method to the active chromatogram (for more details see also chapter Batch ). It is recommended to use absolute paths because the method file will not be searched for in the working directory but in the default directory of the active project.
syntax:

met_apply=PATH\FILENAME

possible values:

A valid path to the method (*.met) file.
implicit value:

None.
example:

clarity.exe met_apply="C:\Users\<user name>\AppData\Local\Temp\CLARITY\1.met"

Open file (*.prm, *.met, *.cal, *.gal, *.seq, *.prj, *.sst, *.nga, *.audit, *.lib and *.dha files)
description:

Opens the specified file(s) on the specified Instrument (using the instrument parameter).
syntax:

PATH\FILENAME

possible values:

The path and filename of the selected file.
implicit value:

Empty.
example:

clarity.exe C:\CLARITY\DataFiles\PROJECTS\Work1.prj or

clarity.exe "C:\CLARITY\DataFiles\DEMO1\Ethanol in blood.seq"

note:

Opened method (*.met file) is propagated only to Single Analysis dialog and is not send to instrument unless Send Method to Instrument option is selected in Method Sending Options dialog in System Configuration.
pass_to_existing_process_only
description:

In case the further command line parameters are wrong, Clarity will not try to open again.

Without the parameter, in case the command line parameters are wrong (e.g. error in the link, extra space, ...), Clarity tries to run anew, which produces error message because just one instance of running Clarity is possible at the same computer.
syntax:

pass_to_existing_process_only

possible values:

None.
implicit value:

None.
example:

clarity.exe pass_to_existing_process_only "C:\CLARITY\DataFiles\DEMO1\Ethanol in blood.seq"

password or p
description:

Tries to log the user on using the password specified. The password used is anonymised in the Audit Trail log.
syntax:

p=STRING

possible values:

String.
implicit value:

Empty.

If empty, the system will deem that the user has an empty password.
example:

clarity.exe user=someuser p=mypassword

prm_close
description:

Closes the active *.prm file opened. If any changes were performed on it, creates the dialog box asking whether these changes should be saved or discarded.
syntax:

prm_close

possible values:

None.
implicit value:

None.
example:

clarity.exe prm_close

prm_close_discard
description:

Closes the active *.prm file opened. If any changes were performed on it, discards the changes in the chromatogram without asking.
syntax:

prm_close_discard

possible values:

None.
implicit value:

None.
example:

clarity.exe prm_close_discard

prm_close_save
description:

Closes the active *.prm file opened. If any changes were performed on it, saves the changes to the chromatogram without asking.
syntax:

prm_close_save

possible values:

None.
implicit value:

None.
example:

clarity.exe prm_close_save

prm_export
description:

Exports the active chromatogram into the specified file. The type of the exported file is determined by its file name extension - supported file types are *.cdf, *.chr, *.txt, *.asc. To learn more about file types Export Chromatogram.
syntax:

prm_export=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe prm_export="C:\Users\<user name>\AppData\Local\Temp\CLARITY\1.chr"

prm_import
description:

Imports the specified file as a chromatogram. The type of a file imported is determined by its name extension - supported file types are *.cdf, *.chr, *.txt, *.asc. To learn more about file types Export Chromatogram. Imported chromatogram is stored in windows \Temp directory under the name import.prm. Existing *.prm file is overwritten without warning.

A method must be used on and saved to the resulting chromatogram during import - we use the method currently selected in the Single Analysis window, so its Integration Table parameters, linked calibration etc. are defined by it. Imported chromatogram is made active.
syntax:

prm_import=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe prm_import="C:\Users\<user name>\AppData\Local\Temp\CLARITY\1.chr"

prm_import_ex
description:

Imports the specified file as a chromatogram. The type of a file imported is determined by its name extension - supported file types are *.cdf, *.chr, *.txt, *.asc. To learn more about file types Export Chromatogram. Imported chromatogram is stored in the \Data directory of the current project under the name fname.prm, where fname is file name part of the imported file. Possible existing *.prm file with the same name is overwritten without warning.

A method must be used on and saved to the resulting chromatogram during import - we use the method currently selected in the Single Analysis window, so its Integration Table parameters, linked calibration etc. are defined by it. Imported chromatogram is made active.
syntax:

prm_import_ex=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe prm_import_ex="C:\Users\<user name>\AppData\Local\Temp\CLARITY\1.chr"

prm_save
description:

Saves the active chromatogram. Use together with the instrument parameter (which is ignored by Clarity Lite) to specify the Instrument whose Chromatogram window holds the chromatogram file you are interested in. Chromatogram file can be opened by specifying its path and filename. It is recommended to use absolute paths.
syntax:

prm_save

possible values:

None.
implicit value:

None.
example:

clarity.exe prm_save

prm_save_as
description:

Saves the active chromatogram under the specified name. Use together with the instrument parameter (which is ignored by Clarity Lite) to specify the Instrument whose Chromatogram window holds the chromatogram file you are interested in. Chromatogram file can be opened by specifying its path and filename. It is recommended to use absolute paths.
syntax:

prm_save_as=PATH\FILENAME

possible values:

A valid path to the chromatogram (*.prm) file.
implicit value:

None.
example:

clarity.exe prm_save_as=C:\CLARITY\DataFiles\Work1\Data\Test.prm

recal_level
description:

Recalibrates the opened calibration file at the specified level with an active chromatogram. The calibration file must be specified in the same command line as recal_level. Value 0 does nothing.
syntax:

recal_level=LEVEL

possible values:

0, 1, ... 20, 21 (Blank)

implicit value:

0
example:

clarity.exe test.cal recal_level=5 Recalibrates the test.cal calibration on the 5th level.

register
description:

Registers Clarity file extensions.
syntax:

register

possible values:

None.
implicit value:

None.
example:

clarity.exe register

report_last_only
description:

Suppresses the BadTrace.txt file at the start of Clarity and sends only one dump file. This function can also be set via the DataApex.ini file that may be stored in Windows directory. Must be used when opening Clarity for the first time, otherwise it is ignored. This parameter is suitable for troubleshooting.
syntax:

report_last_only

possible values:

None.
implicit value:

None.
example:

clarity.exe report_last_only

resume_seq
description:

Resumes the sequence on specified Instrument (the Instrument and sequence file must be opened separately). This parameter is suitable for automatic testing or for LIMS interfacing in combination with seq_import.
syntax:

resume_seq=VALUE

possible values:

1 (for Instrument 1), 2 (for Instrument 2), 4 (for Instrument 3), 8 (for Instrument 4), and their binary combinations.
implicit value:

None.
example:

clarity.exe resume_seq=3 (will resume sequence measurement on Instruments 1 and 2)
run
description:

Runs a single analysis on specified Instrument (which must be opened separately). Single analysis has higher priority than sequence run. This parameter is suitable for automatic testing.
syntax:

run=VALUE

possible values:

1 (for Instrument 1), 2 (for Instrument 2), 4 (for Instrument 3), 8 (for Instrument 4), and their binary combinations.
implicit value:

None.
example:

clarity.exe run=7 (will run single analysis on Instruments 1, 2 and 3)
run_seq
description:

Runs the sequence run on specified Instrument (the Instrument and sequence file must be opened separately). This parameter is suitable for automatic testing or for LIMS interfacing in combination with seq_import.
syntax:

run_seq=VALUE

possible values:

1 (for Instrument 1), 2 (for Instrument 2), 4 (for Instrument 3), 8 (for Instrument 4), and their binary combinations.
implicit value:

None.
example:

clarity.exe run_seq=7 (will run sequence measurement on Instruments 1, 2 and 3)
seq_export
description:

Exports the active sequence into the specified *.txt file.
syntax:

seq_export=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe seq_export="C:\Users\<user name>\AppData\Local\Temp\CLARITY\seq.txt"

seq_export_utf8
description:

Exports the active sequence into the specified *.txt file using UTF8 encoding.
syntax:

seq_export_utf8=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe seq_export_utf8="C:\Users\<user name>\AppData\Local\Temp\CLARITY\seq.txt"

seq_import
description:

Imports the specified *.txt file as a sequence. Current sequence is replaced by imported one, Sequence window is opened. The command is ignored when the sequence is running. Sequence Options dialog is never opened after command line import. Import settings are the same as the last saved ones during manual import. File name of imported sequence is noname, so it is necessary to use seq_save_as to store imported sequence before run.
syntax:

seq_import=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe seq_import="C:\Users\<user name>\AppData\Local\Temp\CLARITY\seq.txt". Examples section below the commands for more information.
seq_import_append
description:

Imports the specified *.txt file as a sequence. Current sequence will be appended with lines from the imported file, Sequence window will be opened and the sequence file will be saved. Can be performed when the sequence is running. Sequence Options dialog is never opened after command line import. Import settings are the same as the last saved ones during manual import.
syntax:

seq_import_append=PATH\FILENAME

possible values:

A valid path and filename.
implicit value:

None.
example:

clarity.exe seq_import_append="C:\Users\<user name>\AppData\Local\Temp\CLARITY\seq.txt"

seq_save
description:

Saves the active sequence. Use together with the instrument parameter to specify the Instrument whose Sequence window holds the sequence file you are interested in. Sequence file can be opened by specifying its path and filename. It is recommended to use absolute paths.
syntax:

seq_save

possible values:

None.
implicit value:

None.
example:

clarity.exe i=2 seq_save - saves the sequence opened in the second Instrument.
seq_save_as
description:

Saves the active sequence under the specified name. Use together with the instrument parameter to specify the Instrument whose Sequence window holds the sequence file you are interested in. Sequence file can be opened by specifying its path and filename. It is recommended to use absolute paths. Command is ignored when sequence is running.
syntax:

seq_save_as=PATH\FILENAME

possible values:

A valid path to the sequence (*.seq) file.
implicit value:

None.
example:

clarity.exe seq_save_as="C:\Users\<user name>\AppData\Local\Temp\CLARITY\results.seq"

set_sample_name
description:

Sets sample name parameter for the next single analysis run. It is possible to set the Instrument by the i=(number of Instrument) parameter.
syntax:

set_sample_name=text

possible values:

Any non-empty text.
implicit value:

None.
example:

clarity.exe set_sample_name="sample name" or

clarity.exe i=2 set_sample_name="sample name"

show_help_id
description:

After calling the context help (via the F1 key or Help button) a message box with the help filename and topic ID will be displayed. Hardware and Control modules need to be configured to the Instrument, otherwise a classical help will be displayed for its dialogs.
syntax:

show_help_id

possible values:

None.
implicit value:

None.
example:

clarity.exe show_help_id

sno or o
description:

Uses the specified serial number (*.sno) file. Must be used when opening Clarity for the first time, otherwise it is ignored.
syntax:

o=PATH\FILENAME

possible values:

The path and filename of the serial number (*.sno) file.
implicit value:

Empty path.

If the path is not specified, the system will look for the serial number (*.sno) file in the \Cfg directory. If not found, the system will then look for the file in the \Bin directory where the clarity.exe file is located.
example:

clarity.exe o=C:\CLARITY\Cfg\clarity.sno

stop
description:

Stops the single analysis/sequence measurement on the specified Instrument. This parameter is suitable for automatic testing. In case of sequence it stops both current acquisition and sequence itself.
syntax:

stop=VALUE

possible values:

1 (for Instrument 1), 2 (for Instrument 2), 4 (for Instrument 3), 8 (for Instrument 4), and their binary combinations.
implicit value:

None.
example:

clarity.exe stop=7 (will stop single analysis/sequence on Instruments 1, 2 and 3)
unregister
description:

Unregisters Clarity file extensions.
syntax:

unregister

possible values:

None.
implicit value:

None.
example:

clarity.exe unregister

user or u
description:

Logs on the specified user.
syntax:

u=STRING

possible values:

String.
implicit value:

Empty.

If empty, the system will show the Login dialog.
example:

clarity.exe u="John Doe"

Clarity will automatically log in the user account called "John Doe".

Examples

Example 1:

This batch file will subsequently open Instrument 1 and Instrument 2. On Instrument 1 it will open the Demo1 project, load the 2506multi.prm chromatogram and Ethanol in blood.seq sequence. On Instrument 2 it will open Pah_epa.cal calibration file.

This batch file can be found in the UTILS subdirectory of the C:\CLARITY\Bin directory under the name CLARITY_commandline_example.bat.

start C:\CLARITY\Bin\clarity.exe i=1 u=Administrator C:\CLARITY\DataFiles\PROJECTS\Demo1.prj C:\CLARITY\DataFiles\DEMO1\DATA\2506multi.prm C:\CLARITY\DataFiles\DEMO1\Ethanol in blood.seq

C:\CLARITY\Bin\UTILS\delay.exe 5

start C:\CLARITY\Bin\clarity.exe i=2 u=Administrator C:\CLARITY\DataFiles\PROJECTS\Demo2.prj C:\CLARITY\DataFiles\DEMO2\CALIB\Pah_epa.cal

Example 2:

This batch file will open the Instrument 1, import 1.chr file as a chromatogram, apply a calibration on it, export the chromatogram and chromatogram results and close the chromatogram (single line command), then it closes Clarity itself. This can be useful when Clarity has to cooperate with other programs, such as LIMS.

start C:\CLARITY\Bin\clarity.exe i=1 u=Administrator

C:\CLARITY\Bin\UTILS\delay.exe 5

start C:\CLARITY\Bin\clarity.exe prm_import_ex="C:\Users\<user name>\AppData\Local\Temp\CLARITY\1.chr" cal_apply="C:\CLARITY\DataFiles\WORK1\Calib\1.cal" prm_export="C:\Users\<user name>\AppData\Local\Temp\CLARITY\export.chr" export_results="C:\Users\<user name>\AppData\Local\Temp\CLARITY\export.txt" prm_close_discard

C:\CLARITY\Bin\UTILS\delay.exe 5

start C:\CLARITY\Bin\clarity.exe exit

Example 3:

This batch file will open Instrument 1 as Administrator, import sequence file stored in C:\CLARITY\DataFiles\WORK1\sequence.txt and save it in the same directory in Clarity file format (*.seq) and finally start the sequence. Before trying this example create the sequence.txt file in the given folder, e.g. using File - Export command in the Sequence window to save existing Clarity sequence to *.txt.

start C:\CLARITY\Bin\clarity.exe i=1 u=Administrator

C:\CLARITY\Bin\UTILS\delay.exe 15

C:\CLARITY\Bin\clarity.exe seq_import=C:\CLARITY\DataFiles\WORK1\sequence.txt

C:\CLARITY\Bin\UTILS\delay.exe 3

C:\CLARITY\Bin\clarity.exe seq_save_as=C:\CLARITY\DataFiles\WORK1\sequence.seq

C:\CLARITY\Bin\UTILS\delay.exe 10

C:\CLARITY\Bin\clarity.exe run_seq=1

Notes:

It is possible to call-up the clarity.exe file when another instance of Clarity is already running. The new instance must quit (because only one running instance of Clarity is allowed at a time). Before quitting this new instance passes parameters to the instance already running. If clarity.exe is already running, the sdk, sno, and cfg parameters will be ignored. If clarity.exe is already running and the specified Instrument is opened, parameters user, password and dsk will be ignored. For all opening files some restrictions apply:

  • A sequence must not be running.
  • There must not be an opened modal dialog.
  • Permission must be obtained to open a method.
  • It must be allowed to change project.

Delay is not a regular batch command, it is a utility that waits a specified amount of time (set in seconds). Delay.exe file can be found in the UTILS directory.

Note:

The necessary delay time that has to be set in the batch file is dependent on the configuration of the station and command line parameters used.

Several restrictions apply to the command line parameters used in the command line or a batch file:

  • Only one project file (*.prj) can be accepted from the command line (actually the first one) for one Instrument.
  • Only one method file (*.met) can be accepted from one command line (actually the first one).
  • Only one sequence file (*.seq) can be accepted from one command line (actually the first one).
  • Multiple chromatograms (*.prm) can be accepted for opening from one command line.
  • Maximum number of characters per command line is limited to 126 characters. Any commands after this limit will not be carried out and Clarity will issue a warning message.
  • Configuration files such as *.cfg, *.sno, *.psw and *.dsk should be located in the same directory as they are interlinked. Placing them each in a different place may result in incorrect behavior.

When opening an Instrument, the first project, method, sequence, calibration and then the chromatogram(s) are opened.