Skyline command line arguments

args.txt

$ docker run -it --rm -v $PWD/:/data/ proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses wine SkylineCmd.exe      
To access the command-line interface for Skyline you can use either SkylineRunner.exe or SkylineCmd.exe.

SkylineRunner.exe is a tiny shim executable less than 10 KB in size.  It requires a Skyline installation, performed with  
the self-updating web installers, on the computer on which SkylineRunner is run.  SkylineRunner simply starts a separate  
Skyline process running without any user interface, pipes the parameter options from the command-line to the running
Skyline instance, and prints output from its Skyline instance to the command console. You can still run multiple instances
of SkylineRunner and it will start multiple instances of Skyline. The Skyline instance started by SkylineRunner is
independent of any other instances that may already be running on the same machine.  It is not necessary to have a visible
instance of Skyline running on your computer for SkylineRunner to work.

SkylineCmd.exe is a much simpler executable which is always installed beside Skyline.exe. It uses the Skyline.exe module  
as a DLL providing a much cleaner command-line implementation than SkylineRunner.exe, but you must know where
SkylineCmd.exe lives on disk to run it, which is usually not the case with the web installer. Usually, you will use either
the "Unplugged" installer or the Administrator installer (or recently the Wine Docker Container for Linux systems) if you 
want to use SkylineCmd.exe. The "Unplugged" installer comes in a ZIP file and you can just unzip it, find SkylineCmd.exe  
and run it in-place. The Administrator installer puts SkylineCmd.exe in C:\Program Files\Skyline.

The Skyline command-line interface is intended for automating tasks such as quality control, scheduling and refinement,
during acquisition.  With the Skyline command-line interface, you can open a Skyline document, import a newly acquired
data file, and export a report or new method. You can also run large-scale chromatogram extraction and peak picking for
proteomewide DIA and DDA experiments faster and consuming less memory than using the full graphic user interface. (See
Webinar 14: https://skyline.ms/webinar14.url)

General input/output
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?Argument                          ?Description                                                                          ?
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?--in=path/to/file.sky             ?Open a Skyline file                                                                  ?
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?--save                            ?Saves any changes to the file                                                        ?
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?--save-settings                   ?Causes settings changes to the global environment, e.g. added reports, libraries,    ?
?                                  ?enzymes, etc. to be saved to the program configuration file.                         ?
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?--out=path/to/file.sky            ?Same as save except writes to the specified file                                     ?
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?--share-zip[=path/to/file.sky.zip]?Saves the entire project (document, results, libraries, etc.) to a ZIP archive.      ?
?                                  ?Defaults to a minimal archive.                                                       ?
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?--share-type=<minimal | complete> ?Specifies the type, 'minimal' or 'complete', of archive to share when --share-zip is ?
?                                  ?specified. Minimal is the default attempting to reduce the size of the archive to the?
?                                  ?minimum necessary to represent the targets in the document while 'complete' maintains?
?                                  ?full fidelity of all project files.                                                  ?
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?--batch-commands=path/to/file     ?Runs a file line by line treating each line like a SkylineRunner/Cmd input. Useful   ?
?                                  ?for automating the execution of multiple commands.  The open Skyline file remains    ?
?                                  ?active through all commands.                                                         ?
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?--dir=path/to/folder              ?Used to specify a default root directory for all other path arguments, other than the?
?                                  ?directory in which the command is run.                                               ?
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?--timestamp                       ?All logging output will be preceded by a time and date.                              ?
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?--memstamp                        ?All logging output will be preceded by two memory usage values managed and process   ?
?                                  ?private bytes in MB, rounded to the nearest MB.                                      ?
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?--log-file=path/to/file           ?Sends all logged output to a file.                                                   ?
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?--help[=<ascii | no-borders>]     ?Shows this text.                                                                     ?
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?--version                         ?Emits version information for the running installation                               ?
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Until the section titled Settings Customization all other command line arguments rely on the '--in' argument because they 
all rely on having a Skyline document open.

Importing results replicates
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?--import-file=path/to/file           ?Attach a replicate to the open document.                                          ?
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?--import-replicate-name=<name>       ?Name to give the new replicate in an -import-file operation.                      ?
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?--import-optimizing=<CE | DP>        ?Indicates the data being imported contains extra transitions for detecting optimal?
?                                     ?collision energy or declustering potential.                                       ?
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?--import-append                      ?Append the import-file to the given replicate. This is an intention check in case ?
?                                     ?the document already has a replicate with the given name. By default this is set  ?
?                                     ?to false. This option only works with the --import-file option.                   ?
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?--import-all=path/to/folder          ?Imports from a folder all files or sub-folders which are not already in the       ?
?                                     ?document, naming each with the base-name of the file or sub-folder, unless the    ?
?                                     ?--import-naming-pattern parameter is also supplied. If --import-replicate-name is ?
?                                     ?supplied, then all files are added to one multi-injection replicate.              ?
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?--import-all-files=path/to/folder    ?Imports from a folder all files but not subfolders which are not already in the   ?
?                                     ?document, naming each with the base-name of the file, unless the                  ?
?                                     ?--import-naming-pattern parameter is also supplied. If --import-replicate-name is ?
?                                     ?supplied, then all files are added to one multi-injection replicate.              ?
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?--import-naming-pattern=<reg-ex>     ?A regular expression from which the first group will be used to name replicates in?
?                                     ?an --import-all operation (e.g. [^_]_(.*) for everything after the first          ?
?                                     ?underscore).                                                                      ?
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?--import-filename-pattern=<reg-ex>   ?A regular expression that is applied to file names to select the ones that will be?
?                                     ?imported.                                                                         ?
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?--import-samplename-pattern=<reg-ex> ?A regular expression that is applied to sample names (e.g. in a multi-injection   ?
?                                     ?.wiff file) to select the ones that will be imported.                             ?
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?--import-before=<date>               ?When importing from a folder, only import from files with modified time before the?
?                                     ?given date.                                                                       ?
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?--import-on-or-after=<date>          ?When importing from a folder, only import from files with modified time on or     ?
?                                     ?after the given date.                                                             ?
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?--import-no-join                     ?Import results files to individual .skyd files without joining them to the main   ?
?                                     ?document .skyd file. This is useful for distributed processing, as on HPC cluster.?
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?--import-process-count=<integer>     ?A number of sub-processes will be run for single-file import, after which the     ?
?                                     ?results from each single file will be joined by the main process. This can produce?
?                                     ?10x performance gains on24-core NUMA servers and 3-4x even on i7 processors, under?
?                                     ?the right conditions. Be sure to test with your system.                           ?
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?--import-threads=<integer>           ?A number of files will be imported in parallel using threads in the main process  ?
?                                     ?(equivalent to "Files to import simultaneously" in the user interface), after     ?
?                                     ?which the results from each single file will be joined. This can produce 2-4x     ?
?                                     ?performance gains under the right conditions. Be sure to test with your system.   ?
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?--import-warn-on-failure             ?If importing a file fails with an error the message is emitted as a warning, the  ?
?                                     ?replicate is removed, and importing continues to completion.                      ?
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?--import-lockmass-positive=<number>  ?Waters lockmass correction m/z for positive ion scans.                            ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--import-lockmass-negative=<number>  ?Waters lockmass correction m/z for negative ion scans.                            ?
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?--import-lockmass-tolerance=<number> ?Waters lockmass correction tolerance m/z.                                         ?
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?--import-peak-boundaries=path/to/file?Read peak boundaries from a comma or tab separated file                           ?
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Reintegrate with advanced peak picking models
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?--reintegrate-model-name=<name> ?The name of a scoring model to use for the reintegrate operation. The model can either ?
?                                ?be pre-defined (e.g. using the Edit > Refine > Reintegrate form) or created            ?
?                                ?automatically during this operation by using --reintegrate-create-model.               ?
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?--reintegrate-create-model      ?This option will cause a new model to be created, using the mProphet algorithm with all?
?                                ?available scores for the results found in the document. (requires                      ?
?                                ?--reintegrate-model-name)                                                              ?
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?--reintegrate-model-type=       ?The type of peak scoring model to train to produce z scores and q values. (dafault     ?
?<mProphet | Skyline | SkylineML>?mProphet) Skyline - simply scales coefficients of the default Skyline model to estimate?
?                                ?a unit normal distribution from the decoys. SkylineML - uses the mProphet machine      ?
?                                ?learning algorithm to train a model using only the default set of feature scores.      ?
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?--reintegrate-model-second-best ?Forces the use of second best peaks during reintegration. The default is to use decoys ?
?                                ?only.                                                                                  ?
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?--reintegrate-model-both        ?Forces the use of both decoys and second best peaks during reintegration. The default  ?
?                                ?is to use decoys only.                                                                 ?
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?--reintegrate-overwrite-peaks   ?Existing manually integrated peaks will be overwritten with peaks chosen by the        ?
?                                ?reintegration model. (requires --reintegrate-model-name)                               ?
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?--reintegrate-exclude-feature=  ?Use to exclude a particular feature score by name from the model. Names can be found in?
?<feature name>                  ?the user interface. This argument may be used multiple times to exclude multiple       ?
?                                ?features.                                                                              ?
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Removing results replicates
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?--remove-before=<date>?Remove all results from the open document with an acquired time before the given date.           ?
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?--remove-all          ?Remove all results from the open document.                                                       ?
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Minimizing results file size
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?--chromatograms-limit-noise=<number>?Limits the length of the chromatagrams to a number of minutes around the           ?
?                                    ?chromatogram peak, i.e. ? minutes.                                                 ?
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?--chromatograms-discard-unused      ?Discard all unused chromatograms from the document.                                ?
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Importing other Skyline documents
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?--import-document=path/to/file.sky  ?Import another Skyline document file into the open document. This may be specified ?
?                                    ?multiple times for multiple files.                                                 ?
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?--import-document-results=          ?Determines how any results in the imported document are handled. The default is to ?
?<remove | merge_names |             ?remove them.                                                                       ?
?merge_indices | add>                ?                                                                                   ?
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?--import-document-merge-peptides    ?Matching peptides are merged if used, otherwise not.                               ?
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Importing annotations
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?--import-annotations=path/to/file.csv?Imports annotations from a CSV file into the document. Use File > Export >        ?
?                                     ?Annotations to create example files of the required format with paths to associate?
?                                     ?the annotations to document elements.                                             ?
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Importing FASTA files
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?--import-fasta=path/to/file?Import a FASTA file into the open document.                                                 ?
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?--keep-empty-proteins      ?Keeps any empty proteins in the open document after importing a FASTA file.                 ?
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Importing peptide searches
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?--import-search-file=path/to/file      ?Import a peptide search results file into the open document, building a         ?
?                                       ?document-specific spectral library. This may be specified multiple times for    ?
?                                       ?multiple files. Use -import-fasta argument to add matched peptides as targets.  ?
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?--import-search-cutoff-score=<number>  ?Defines a cutoff score (between 0 and 1) to be used when building a spectral    ?
?                                       ?library from peptide search results files, where 1 is for highest confidence    ?
?                                       ?matches and 0 includes everything. [default 0.95]                               ?
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?--import-search-irts=<name>            ?Name of iRT standard to to be used when building a spectral library.            ?
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?--import-search-num-cirts=<integer>    ?Specify the number of CiRT peptides to use as iRT standards if building a       ?
?                                       ?spectral library with CiRT peptides as iRT standards.                           ?
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?--import-search-recalibrate-irts       ?If building a spectral library with iRT standards, recalibrate the iRT standard ?
?                                       ?values relative to the peptides being added.                                    ?
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?--import-search-add-mods               ?Adds all modifications found in peptide search results files to the open        ?
?                                       ?document.                                                                       ?
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?--import-search-include-ambiguous      ?Prevent spectra with multiple ambiguous peptide matches from being discarded    ?
?                                       ?when building the spectral library.                                             ?
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?--import-search-prefer-embedded-spectra?For MaxQuant msms.txt files to force use of the spectra in the file rather than ?
?                                       ?opening raw data files for the original spectra. The MaxQuant msms.txt files    ?
?                                       ?contain charge-state deconvoluted spectra which may not be appropriate for      ?
?                                       ?target selection.                                                               ?
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Importing transition lists and assay libraries
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?--import-transition-list=path/to/file ?Import a simple transition list with Q1, Q3 and peptide sequence.  Also supports ?
?                                      ?molecule transition lists in CSV format with suitable headers.                   ?
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?--import-assay-library=path/to/file   ?Import an assay library transition list with columns for iRT and relative product?
?                                      ?ion abundance to create an iRT calculator and spectral library for enhanced peak ?
?                                      ?picking.                                                                         ?
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?--ignore-transition-errors            ?When present imports all recognized transitions from a transition list or assay  ?
?                                      ?library, with error rows reported as warnings.                                   ?
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?--irt-standards-group-name=<name>     ?The name of a protein or peptide list containing the iRT standards within an     ?
?                                      ?imported assay library. (optional)                                               ?
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?--irt-standards-file=path/to/file     ?The path to a separate assay library containing the iRT standards to be applied  ?
?                                      ?to an imported assay library. (optional)                                         ?
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?--irt-database-path=path/to/file.irtdb?The path to an existing iRT calculator (.irtdb file) to be used with an imported ?
?                                      ?assay library. Or, if -irt-standards-group-name or -irt-standards-file are used, ?
?                                      ?then this is the output path for the created .irtdb file. (optional) The default ?
?                                      ?iRT calculator path is path/to/document.irtdb                                    ?
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?--irt-calc-name=<name>                ?The name for the iRT calculator created during assay library import. (optional)  ?
?                                      ?The default name is the document base name.                                      ?
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Adding spectral libraries
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?--add-library-path=path/to/file?Specify a spectral library to be added to the open document.                            ?
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?--add-library-name=<name>      ?Name to give the spectral library in an --add-library-path operation.                   ?
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Adding decoy peptides
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?--decoys-add[=<reverse | shuffle>]?Add decoys to a template document for reintegrate model generation with mProphet.    ?
?                                  ?(decoy generation method is optional and defaults to "reverse")                      ?
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?--decoys-add-count=<integer>      ?A number of decoys to add. (optional - default is to generate as many decoys as      ?
?                                  ?targets)                                                                             ?
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?--decoys-discard                  ?Forces any existing decoys to be discarded when --decoys-add is used.                ?
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Refining the targets list
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?--refine-min-peptides=<integer>   ?Proteins with fewer than this number of peptides will be                             ?
?                                  ?removed from the document.                                                           ?
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?--refine-remove-repeats           ?All repeated peptides will be removed to leave only the                              ?
?                                  ?first occurrence of any peptide.                                                     ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-remove-duplicates        ?All peptides that are not unique within the document                                 ?
?                                  ?will be removed.                                                                     ?
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?--refine-missing-library          ?All targets that do not correspond to a library match will be removed.               ?
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?--refine-min-transitions=<integer>?Precursors with fewer than this number of transitions will be                        ?
?                                  ?removed from the document.                                                           ?
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?--refine-label-type=<label type>  ?Precursors of the specified isotope label type will be removed (default) or added if ?
?                                  ?--refine-add-label-type is also used.                                                ?
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?--refine-add-label-type           ?Add back precursors of an isotope label type.                                        ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-auto-select-peptides     ?All proteins will be reset to auto-select the peptides they contain.                 ?
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?--refine-auto-select-precursors   ?All peptides will be reset to auto-select the precursors they contain.               ?
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?--refine-auto-select-transitions  ?All precursors will be reset to auto-select the transitions they contain.            ?
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Refining the targets list based on imported results
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?--refine-min-peak-found-ratio=              ?All elements with peak found ratio below this number                       ?
?<number>                                    ?will be removed from the document:                                         ?
?                                            ?                                                                           ?
?                                            ?Green = 1.0                                                                ?
?                                            ?Orange &gt;= 0.5                                                           ?
?                                            ?Red &lt; 0.5                                                               ?
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?--refine-max-peak-found-ratio=              ?All elements with peak found ratio above this number                       ?
?<number>                                    ?will be removed from the document:                                         ?
?                                            ?                                                                           ?
?                                            ?Green = 1.0                                                                ?
?                                            ?Orange &gt;= 0.5                                                           ?
?                                            ?Red &lt; 0.5                                                               ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-max-peptide-peak-rank=             ?All transitions with an average area peak ranking                          ?
?<integer>                                   ?greater than this number will be removed from the                          ?
?                                            ?document.                                                                  ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-max-transition-peak-rank=          ?All transitions with an average area peak ranking                          ?
?<integer>                                   ?greater than this number will be removed from the                          ?
?                                            ?document.                                                                  ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-max-precursor-only                 ?Only the precursor charge state with the maximum peak area will be         ?
?                                            ?retained.                                                                  ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-prefer-larger-products             ?Causes refinement to choose larger product ions                            ?
?                                            ?when smaller, less selective ions yeild only fractionally                  ?
?                                            ?greater peak area.                                                         ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-missing-results                    ?All elements without measured results will be                              ?
?                                            ?removed from the document.                                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-min-time-correlation=              ?Precursors will be removed from the document                               ?
?<number>                                    ?until the target value for the correlation coefficient of a linear         ?
?                                            ?regression with the optimal retention time calculator                      ?
?                                            ?exceed this threshold.                                                     ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-min-dotp=<number>                  ?All precursors with a product ion peak area to library                     ?
?                                            ?spectrum dot-product below this threshold will be removed                  ?
?                                            ?from the document.                                                         ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-min-idotp=<number>                 ?All precursors with a MS1 precursor peak area to expected                  ?
?                                            ?isotope distribution dot-product below this threshold will be              ?
?                                            ?removed from the document.                                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-use-best-result                    ?Use only the best replicate for each peptide in refinement value           ?
?                                            ?calculations. (use for fractionation)                                      ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-cv-remove-above-cutoff=<number>    ?All target precursors with peak area CV above the cutoff will be removed.  ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-cv-global-normalize=               ?Areas used in CV calculations are normalized as specified. (default no     ?
?<global_standards | equalize_medians | tic> ?normalization)                                                             ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-cv-reference-normalize=            ?Areas used in CV calculations are normalized to a reference type, e.g.     ?
?<label type>                                ?"heavy".                                                                   ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-cv-transitions=<all | best>        ?Specifies the transitions for which peak areas are summed and used in CV   ?
?                                            ?calculations for CV refinement. (either all or a single best transition)   ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-cv-transitions-count=<integer>     ?Specifies the count of transitions selected by library transition rank     ?
?                                            ?(isotopes for precursors and library for fragments) for which peak areas   ?
?                                            ?are summed and used in CV calculations for CV refinement.                  ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-cv-ms-level=<precursors | products>?The MS level used in the CV calculations. Defaults to "products" which will?
?                                            ?usually have lower CVs than precursors in methods like PRM and DIA.        ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-qvalue-cutoff=<number>             ?All target precursors with a maximum detection q value above the cutoff    ?
?                                            ?will be removed. If --refine-minimum-detections is used then at least the  ?
?                                            ?specified number of replicates must have a detection q value below the     ?
?                                            ?cutoff.                                                                    ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-minimum-detections=<integer>       ?All target precursors with less than the specified number of replicates    ?
?                                            ?with detection q value below the --refine-qvalue-cutoff are removed.       ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-gc-p-value-cutoff=<number>         ?Keep only targets with a group comparison adjusted p value below the       ?
?                                            ?specified cut-off. (required for group comparison refinement)              ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-gc-fold-change-cutoff=<number>     ?Keep only targets with a group comparision fold change above this cutoff.  ?
?                                            ?(optional for group comparison refinement)                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-gc-ms-level=<number>               ?The MS level (1 or 2) to use in calculating peak areas for a group         ?
?                                            ?comparison refinement. Defaults to level 2 if both levels are present, and ?
?                                            ?otherwise uses whichever level is present.                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--refine-gc-name=<label type>               ?The name of a previously defined group comparison to use in refining for   ?
?                                            ?significantly changing targets. Specify the argument multiple times with   ?
?                                            ?multiple names to keep the union of multiple comparisons.                  ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????

Exporting reports
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--report-name=<name>          ?The name of a report to export as it appears in the Skyline Export Report form.          ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--report-file=path/to/file.csv?The path to export the report to. Required if --report-name is specified.                ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--report-add=path/to/file.skyr?Add reports from a saved report template file to the running program.                    ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--report-conflict-resolution= ?Specifies how to resolve report name conflicts, by either overwriting or skipping them,  ?
?<overwrite | skip>            ?when using --report-add (default is to output an error message for conflicts)            ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--report-format=<csv | tsv>   ?CSV for comma-separated reports (or semicolon separated, depending on your localization) ?
?                              ?or TSV for tab separated reports [default CSV]                                           ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--report-invariant            ?Exports the report with the "Invariant" language setting, using English (US) number      ?
?                              ?formats and header text without spaces, ideal for use with the R statistical programming ?
?                              ?environment.                                                                             ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????

Exporting chromatograms
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--chromatogram-file=path/to/file.tsv?The path to the tab delimited file to export chromatograms to. Defaults to         ?
?                                    ?exporting precursors and products.                                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--chromatogram-precursors           ?Export precursor ion chromatograms. Requires the --chromatogram-file argument.     ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--chromatogram-products             ?Export product ion chromatograms. Requires the --chromatogram-file argument.       ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--chromatogram-base-peaks           ?Export base peak chromatograms. Requires the --chromatogram-file argument.         ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--chromatogram-tics                 ?Export total ion current chromatograms. Requires the --chromatogram-file argument. ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????

Exporting isolation/transition lists
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-isolationlist-instrument=   ?Export an isolation list. This option is required for exporting an isolation list and?
?<Agilent QTOF | SCIEX QTOF |      ?has no default. This option cannot be used with --exp-translist-instrument or        ?
?Bruker timsTOF | Thermo Q Exactive?-exp-method-instrument, because you cannot export an isolation list and a transition ?
?| Thermo Fusion | Waters Synapt   ?list or method simultaneously.                                                       ?
?(trap) | Waters Synapt (transfer) ?                                                                                     ?
?| Waters Xevo QTOF>               ?                                                                                     ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-translist-instrument=       ?Export a transition list. This option is required for exporting a transition list and?
?<Agilent | Bruker | SCIEX |       ?has no default. This option cannot be used with --exp-isolation-list or              ?
?Shimadzu | Thermo | Thermo        ?--exp-method-instrument, because you cannot export a transition list and an isolation?
?Quantiva | Thermo Altis | Waters> ?list or method simultaneously.                                                       ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????

Exporting native instrument methods
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-method-instrument=          ?Export a method. This option is required for exporting a method and has no default.  ?
?<Agilent 6400 Series | Bruker QTOF?This option cannot be used with --exp-isolationlist-instrument or                    ?
?| Bruker timsTOF | SCIEX QTRAP |  ?--exp-translist-instrument, because you cannot export a method and an                ?
?SCIEX QTOF | Shimadzu | Thermo TSQ?isolation/transition list simultaneously.                                            ?
?| Thermo LTQ | Thermo Quantiva |  ?                                                                                     ?
?Thermo Altis | Thermo Exploris |  ?                                                                                     ?
?Thermo Fusion | Waters Xevo TQ |  ?                                                                                     ?
?Waters Quattro Premier>           ?                                                                                     ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-template=path/to/file       ?Path of the method template. This can be a file or a directory depending on your     ?
?                                  ?instrument. This option is required for method export.                               ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????

Method and transition list options
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-file=path/to/file               ?Path to the method or transition list file (or directory) to export to. This     ?
?                                      ?option is required for method and transition list export.                        ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-strategy=                       ?Strategy for dividing a method into injections. The default is "single".         ?
?<Single | Protein | Buckets>          ?                                                                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-method-type=                    ?Sets a standard, scheduled or triggered method. The default is "standard".       ?
?<Standard | Scheduled | Triggered>    ?                                                                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-max-trans=<name>                ?Maximum number of transitions per injection for export strategies "protein" and  ?
?                                      ?"buckets" OR maximum number of simultaneous transitions for scheduled methods.   ?
?                                      ?The default is 100.                                                              ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-optimizing=<CE | DP>            ?Export a method with extra transitions for finding optimal collision energy or   ?
?                                      ?declustering potential.                                                          ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-scheduling-replicate=<name>     ?Use this only if creating a scheduled or triggered method. The default is to     ?
?                                      ?schedule based on an average of all replicates, but if you specify one, the      ?
?                                      ?method will be scheduled based on that replicate.                                ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-order-by-mz                     ?Order exported method by m/z values in ascending order (precursor m/z, then      ?
?                                      ?product m/z when applicable) for optimized quadrupole switching.                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-ignore-proteins                 ?Ignore protein boundaries in creating methods.                                   ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-primary-count=<integer>         ?For --exp-method-type=triggered specifies the number of transitions to make      ?
?                                      ?primary.                                                                         ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--exp-polarity=                       ?Controls export behavior for documents with both positive and negative           ?
?<all | positive | negative | separate>?transitions. Allows for output of only positive or only negative transitions, or ?
?                                      ?creates separate outputs for each polarity. Defaults to all, and is ignored for  ?
?                                      ?single polarity documents.                                                       ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????

Vendor-specific method and transition list options
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?Agilent ?--exp-dwell-time=<millis> ?Dwell time per transition. This option is required for unscheduled transition lists.?
?SCIEX   ?                          ?                                                                                    ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?Thermo  ?--exp-add-energy-ramp     ?Adds an extra column for energy ramp to the transition list.  Optional. Defaults to ?
?        ?                          ?false.                                                                              ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?Thermo  ?--exp-use-s-lens          ?Adds an extra column for SLens (which defaults to 50) to the transition list.       ?
?        ?                          ?Optional. Defaults to false.                                                        ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?Thermo  ?--exp-run-length=<minutes>?Run length of the entire gradient in minutes. This option is required for           ?
?Waters  ?                          ?unscheduled experiments.                                                            ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????

Publishing to Panorama
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--panorama-server=<server url>  ?URL of the Panorama server to which the --in file is to be published. The URL should   ?
?                                ?contain the protocol (http or https), hostname and port, if required. Examples:        ?
?                                ?https://panoramaweb.org                                                                ?
?                                ?or                                                                                     ?
?                                ?http://localhost:8080                                                                  ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--panorama-username=<username>  ?The username/email address for a user with access to publish to the Panorama server.   ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--panorama-password=<password>  ?The password for a user with access to publish to the Panorama server.                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--panorama-folder=path/to/folder?The path to a folder on the Panorama server to which the file is to be published (e.g. ?
?                                ?MyProject/MyFolder).                                                                   ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
If the arguments above are used along with arguments to import results files into the document (--import-file or
--import-all) the Skyline document will be uploaded to the given Panorama server only if new results are added to the
document.

Document Settings
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tran-precursor-ion-charges=     ?A comma-separated list of precursor ion charge states to apply to peptide molecules  ?
?"1, 2, 3..."                      ?to generate precursor targets. Changes the transition filter settings for the open   ?
?                                  ?document.                                                                            ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tran-product-ion-charges=       ?A comma-separated list of product ion charge states to apply to peptide fragments to ?
?"1, 2, 3..."                      ?generate product ion transitions. Changes the transition filter settings for the open?
?                                  ?document.                                                                            ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tran-product-ion-types=         ?A comma-separated list of product ion types expected in peptide fragmentation to     ?
?"a, b, c, x, y, z, p"             ?generate product ion transitions. Changes the transition filter settings for the open?
?                                  ?document.                                                                            ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tran-predict-ce=                ?Changes the transition settings collision energy prediction setting to one of the    ?
?<None | Agilent QQQ | SCIEX |     ?previously defined options.                                                          ?
?Shimadzu QQQ | Thermo TSQ Quantiva?                                                                                     ?
?| Thermo TSQ Ultra | Thermo TSQ   ?                                                                                     ?
?Vantage | Waters Xevo>            ?                                                                                     ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tran-predict-dp=                ?Changes the transition settings declustering potential prediction setting to one of  ?
?<None | SCIEX>                    ?the previously defined options.                                                      ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tran-predict-cov=               ?Changes the transition settings compensation voltage prediction setting to one of the?
?<None | SCIEX>                    ?previously defined options.                                                          ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tran-predict-optdb=             ?Changes the transition settings optimization library used in predicting instrument   ?
?<None>                            ?parameters to one of the previously defined options.                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--full-scan-precursor-res=        ?Resolving power of the precursor mass analyzer. If the mass analyzer is 'Centroided' ?
?<resolving power>                 ?the value is in PPM.                                                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--full-scan-precursor-res-mz=     ?The m/z value at which the precursor mass analyzer resolving power is specified.     ?
?<m/z value>                       ?(applies only to orbitrap and ft_icr mass analyzers)                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--full-scan-product-res=          ?Resolving power of the product mass analyzer. If the mass analyzer is 'Centroided'   ?
?<resolving power>                 ?the value is in PPM.                                                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--full-scan-product-res-mz=       ?The m/z value at which the product mass analyzer resolving power is specified.       ?
?<m/z value>                       ?(applies only to orbitrap and ft_icr mass analyzers)                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--full-scan-rt-filter-tolerance=  ?The number of minutes on either side of the predicted time or MS/MS IDs, i.e. ?      ?
?<minutes>                         ?minutes.                                                                             ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--ims-library-res=                ?Resolving power of ion mobility dimension used to filter around ion mobility values  ?
?<resolving power>                 ?from the spectral libraries.                                                         ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????

Tools Installation
The arguments below can be used to install tools onto the Tools menu and do not rely on the '--in' argument because they  
independent of a specific Skyline document.
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-add=<name>                  ?The name of a tool to be added by its settings rather than an installation ZIP file.?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-command=<command | url>     ?The command or webpage URL to run for a command being added by its settings rather  ?
?                                   ?than an installation ZIP file.                                                      ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-arguments="<arguments>"     ?Optional command-line arguments for the tool to be added, used when the tool is     ?
?                                   ?executed. (Not applicable to web URL commands)                                      ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-initial-dir=path/to/folder  ?Optional initial directory for the tool to be added, used when the tool is executed.?
?                                   ? (Not applicable to web URL commands)                                               ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-conflict-resolution=        ?Tells how to resolve a tool name conflict, by either overwriting an existing        ?
?<overwrite | skip>                 ?installation or skipping installation of the new tool.                              ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-report=<report name>        ?The name of a report in the settings to use as the input report for the tool.       ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-output-to-immediate-window  ?When present the tool output is piped to the Immediate Window at runtime.           ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-add-zip=path/to/file.zip    ?Import tools from a tool installation ZIP file.                                     ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-zip-conflict-resolution=    ?Specify whether tool conflicts from the provided ZIP file should be resolved by     ?
?<overwrite | parallel>             ?overwriting or installing in parallel. This is for conflicts related to tool        ?
?                                   ?versioning and report names.                                                        ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-zip-overwrite-annotations=  ?Specify whether conflicting custom annotations from the provided ZIP file should    ?
?<true | false>                     ?overwrite (true) existing annotations or be skipped (false).                        ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-program-macro=              ?Specifies a program title and version to use with the --tool-program-path command.  ?
?<program title>[,<program version>]?Together these commands are for importing tools from a ZIP file that use the        ?
?                                   ?$(ProgramPath()) macro as their command. For more information see the documentation ?
?                                   ?on External Tools. e.g.                                                             ?
?                                   ?--tool-program-macro=R,2.15.2                                                       ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-program-path=path/to/file   ?Specifies the path to an executable on the local machine for the program title and  ?
?                                   ?version specified by the --tool-program-macro flag.                                 ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
?--tool-ignore-required-packages    ?Ignore required packages when installing a tool from a ZIP file.                    ?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????