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Detailed usage instruction
Oliver Maus edited this page Mar 25, 2022
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4 revisions
The general command line structure is designed as either
arc <top-level-command> <top-level-command-args>e.g.
arc initor
arc <object> <subcommand-verb> <subcommand-verb-args>where <object> is one of the following:
assay-
studyor its sub-objects -
investigationor its sub-objects configuration
and <subcommand-verb> models what to do with the object, e.g
arc study initwill initialize a new empty study in the ARC.
while not all object subcommands support all verbs, here is a list of the verbs and what to expect when they are applicable for an <object>:
- arc
<object>init : will initialize a new empty<object>in the ARC. - arc
<object>create will create a new<object>with the passed arguments in the ARC. - arc
<object>update will update the registration of an existing<object>with the passed arguments. - arc
<object>edit will open an existing<object>with a text editor, allowing editing the registration of the<object>. - arc
<object>register will register an existing<object>in the ARC with the passed arguments. - arc
<object>add is the combination of create/init+update and register, meaning it will create a new<object>in the ARC and subsequently register it with the passed arguments - arc
<object>delete will delete the<object>from the arc file structure. - arc
<object>unregister will remove the<object>from the ARC's register. - arc
<object>remove is the combination of delete and unregister, meaning it will delete the<object>from the ARC file structure and the ARC's registry - arc
<object>move will move the<object>from source to target register. - arc
<object>list will print all<object>sregistered in the ARC. - arc
<object>set will set a single value in the<object>. - arc
<object>unset will remove a single value from the<object>.
Here is the current help dump from the command line tool:
USAGE: arc [--help] [--workingdir <working directory>] [--verbosity <verbosity>]
[<subcommand> [<options>]]
SUBCOMMANDS:
init <init args> Initializes basic folder structure
investigation, i <verb and args>
Investigation file functions
study, s <verb and args>
Study functions
assay, a <verb and args>
Assay functions
configuration, config <verb and args>
Configuration editing
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--workingdir, -p <working directory>
Set the base directory of your ARC
--verbosity, -v <verbosity>
Sets the amount of additional printed information: 0->No information, 1 (Default) -> Basic
Information, 2 -> Additional information
--help display this list of options.USAGE: arc init [--help] [--owner <owner>] [--repositoryadress <repository adress>] [--editorpath <editor path>]
OPTIONS:
--owner <owner> Owner of the arc
--repositoryadress <repository adress>
Github adress
--editorpath <editor path>
The path leading to the editor used for text prompts (Default in Windows is notepad)
--help display this list of options.USAGE: arc.exe investigation [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
create <create args> Create a new investigation with the given Metadata
update <update args> Update the ARC's investigation with the given Metdadata
edit Open an editor window to directly edit the ARC's investigation file
delete <delete args> Delete the ARC's investigation file (DANGER ZONE!)
person <person verbs> Person functions
publication <publication verbs>
Publication functions
show Get the values of the ARC's investigation
Use 'arc.exe <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options.
OPTIONS:
--help display this list of options.USAGE: arc investigation create [--help] --identifier <investigation identifier> [--title <title>]
[--description <description>] [--submissiondate <submission date>]
[--publicreleasedate <public release date>]
OPTIONS:
--identifier <investigation identifier>
A identifier or an accession number provided by a repository. This SHOULD be locally unique.
--title <title> A concise name given to the investigation.
--description <description>
A textual description of the investigation.
--submissiondate <submission date>
The date on which the investigation was reported to the repository.
--publicreleasedate <public release date>
The date on which the investigation was released publicly.
--help display this list of options.Give new metadata that overwrite the current metadata of an investigation.
USAGE: arc investigation update [--help] --identifier <investigation identifier> [--title <title>]
[--description <description>] [--submissiondate <submission date>]
[--publicreleasedate <public release date>]
OPTIONS:
--identifier <investigation identifier>
A identifier or an accession number provided by a repository. This SHOULD be locally unique.
--title <title> A concise name given to the investigation.
--description <description>
A textual description of the investigation.
--submissiondate <submission date>
The date on which the investigation was reported to the repository.
--publicreleasedate <public release date>
The date on which the investigation was released publicly.
--help display this list of options.Take the current metadata of an investigation and change it.
(While investigation edit opens the current metadata that can be altered by the user, investigation update will take a new set of metadata and overwrites the existing one)
USAGE: arc investigation edit [--help]
OPTIONS:
--identifier <study identifier>
A unique identifier, either a temporary identifier supplied by users or one generated by a
repository or other database. For example, it could be an identifier complying with the LSID
specification.
--help display this list of options.
USAGE: arc investigation delete [--help] --identifier <investigation identifier>
OPTIONS:
--identifier <investigation identifier>
DangerZone: In order to delete this investigation file please provide its identifier here.
--help display this list of options.USAGE: arc investigation person [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
update <update args> Update an existing person in the arc investigation with the given person metadata. The person is
identified by the full name (first name, last name, mid initials)
edit <edit args> Open and edit an existing person in the arc investigation with a text editor. The person is
identified by the full name (first name, last name, mid initials)
register <register args>
Register a person in the arc investigation with the given assay metadata.
unregister <remove args>
Unregister a person from the given investigation. The person is identified by the full name (first
name, last name, mid initials).
show <show args> Show the metadata of a person registered in the arc investigation
list List all persons registered in the arc investigation
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options.OPTIONS:
--lastname, -l <last name>
The last name of a person associated with the investigation.
--firstname, -f <first name>
The first name of a person associated with the investigation.
--midinitials, -m <mid initials>
The middle initials of a person associated with the investigation.
--email <e mail> The email address of a person associated with the investigation.
--phone <phone number>
The telephone number of a person associated with the investigation.
--fax <fax number> The fax number of a person associated with the investigation.
--address <adress> The address of a person associated with the investigation.
--affiliation <affiliation>
The organization affiliation for a person associated with the investigation.
--roles <roles> Term to classify the role(s) performed by this person in the context of the investigation, which
means that the roles reported here need not correspond to roles held withing their affiliated
organization. Multiple annotations or values attached to one person can be provided by using a
semicolon (";") Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor). The term can be
free text or from, for example, a controlled vocabulary or an ontology. If the latter source is used
the Term Accession Number and Term Source REF fields below are required.
--rolestermaccessionnumber <roles term accession number>
The accession number from the Term Source associated with the selected term.
--rolestermsourceref <roles term source ref>
dentifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Names declared in the Ontology Source Reference section.
--help display this list of options.USAGE: arc investigation person edit [--help] --lastname <last name> --firstname <first name>
[--midinitials <mid initials>]
OPTIONS:
--lastname, -l <last name>
The last name of a person associated with the investigation.
--firstname, -f <first name>
The first name of a person associated with the investigation.
--midinitials, -m <mid initials>
The middle initials of a person associated with the investigation.
--help display this list of options.USAGE: arc investigation person register [--help] --lastname <last name> --firstname <first name>
[--midinitials <mid initials>] [--email <e mail>]
[--phone <phone number>] [--fax <fax number>] [--address <adress>]
[--affiliation <affiliation>] [--roles <roles>]
[--rolestermaccessionnumber <roles term accession number>]
[--rolestermsourceref <roles term source ref>]
OPTIONS:
--lastname, -l <last name>
The last name of a person associated with the investigation.
--firstname, -f <first name>
The first name of a person associated with the investigation.
--midinitials, -m <mid initials>
The middle initials of a person associated with the investigation.
--email <e mail> The email address of a person associated with the investigation.
--phone <phone number>
The telephone number of a person associated with the investigation.
--fax <fax number> The fax number of a person associated with the investigation.
--address <adress> The address of a person associated with the investigation.
--affiliation <affiliation>
The organization affiliation for a person associated with the investigation.
--roles <roles> Term to classify the role(s) performed by this person in the context of the investigation, which
means that the roles reported here need not correspond to roles held withing their affiliated
organization. Multiple annotations or values attached to one person can be provided by using a
semicolon (";") Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor). The term can be
free text or from, for example, a controlled vocabulary or an ontology. If the latter source is used
the Term Accession Number and Term Source REF fields below are required.
--rolestermaccessionnumber <roles term accession number>
The accession number from the Term Source associated with the selected term.
--rolestermsourceref <roles term source ref>
dentifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Names declared in the Ontology Source Reference section.
--help display this list of options.USAGE: arc investigation person register [--help] --lastname <last name> --firstname <first name>
[--midinitials <mid initials>] [--email <e mail>]
[--phone <phone number>] [--fax <fax number>] [--address <adress>]
[--affiliation <affiliation>] [--roles <roles>]
[--rolestermaccessionnumber <roles term accession number>]
[--rolestermsourceref <roles term source ref>]
OPTIONS:
--lastname, -l <last name>
The last name of a person associated with the investigation.
--firstname, -f <first name>
The first name of a person associated with the investigation.
--midinitials, -m <mid initials>
The middle initials of a person associated with the investigation.
--email <e mail> The email address of a person associated with the investigation.
--phone <phone number>
The telephone number of a person associated with the investigation.
--fax <fax number> The fax number of a person associated with the investigation.
--address <adress> The address of a person associated with the investigation.
--affiliation <affiliation>
The organization affiliation for a person associated with the investigation.
--roles <roles> Term to classify the role(s) performed by this person in the context of the investigation, which
means that the roles reported here need not correspond to roles held withing their affiliated
organization. Multiple annotations or values attached to one person can be provided by using a
semicolon (";") Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor). The term can be
free text or from, for example, a controlled vocabulary or an ontology. If the latter source is used
the Term Accession Number and Term Source REF fields below are required.
--rolestermaccessionnumber <roles term accession number>
The accession number from the Term Source associated with the selected term.
--rolestermsourceref <roles term source ref>
dentifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Names declared in the Ontology Source Reference section.
--help display this list of options.USAGE: arc investigation person show [--help] --lastname <last name> --firstname <first name>
[--midinitials <mid initials>]
OPTIONS:
--lastname, -l <last name>
The last name of a person associated with the investigation.
--firstname, -f <first name>
The first name of a person associated with the investigation.
--midinitials, -m <mid initials>
The middle initials of a person associated with the investigation.
--help display this list of options.USAGE: arc investigation publication [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
update <update args> Update an existing publication in the arc investigation with the given publication metadata. The
publication is identified by the doi
edit <edit args> Open and edit an existing publication in the arc investigation with a text editor. The publication
is identified by the doi
register <register args>
Register a publication in the arc investigation with the given assay metadata.
unregister <remove args>
Unregister a publication from the given investigation. The publication is identified by the doi
show <show args> Show the metadata of a publication registered in the arc investigation
list List all publication registered in the arc investigation
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options. USAGE: arc investigation publication update [--help] --doi <doi> [--pubmedid <pubmed id>]
[--authorlist <author list>] [--title <publication title>]
[--status <publication status>]
[--statustermaccessionnumber <publication status term accession number>]
[--statustermsourceref <publication status term source ref>]
OPTIONS:
--doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available).
--pubmedid, -p <pubmed id>
The PubMed IDs of the described publication(s) associated with this investigation.
--authorlist <author list>
The list of authors associated with that publication.
--title <publication title>
The title of publication associated with the investigation.
--status <publication status>
A term describing the status of that publication (i.e. submitted, in preparation, published).
--statustermaccessionnumber <publication status term accession number>
The accession number from the Term Source associated with the selected term.
--statustermsourceref <publication status term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one the Term Source Name declared in the in the Ontology Source Reference section.
--help display this list of options. USAGE: arc investigation publication edit [--help] --doi <doi>
OPTIONS:
--doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available).
--help display this list of options. USAGE: arc investigation publication register [--help] --doi <doi> [--pubmedid <pubmed id>]
[--authorlist <author list>] [--title <publication title>]
[--status <publication status>]
[--statustermaccessionnumber <publication status term accession number>]
[--statustermsourceref <publication status term source ref>]
OPTIONS:
--doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available).
--pubmedid, -p <pubmed id>
The PubMed IDs of the described publication(s) associated with this investigation.
--authorlist <author list>
The list of authors associated with that publication.
--title <publication title>
The title of publication associated with the investigation.
--status <publication status>
A term describing the status of that publication (i.e. submitted, in preparation, published).
--statustermaccessionnumber <publication status term accession number>
The accession number from the Term Source associated with the selected term.
--statustermsourceref <publication status term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one the Term Source Name declared in the in the Ontology Source Reference section.
--help display this list of options. USAGE: arc investigation publication unregister [--help] --doi <doi>
OPTIONS:
--doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available).
--help display this list of options. USAGE: arc investigation publication show [--help] --doi <doi>
OPTIONS:
--doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available).
--help display this list of options. USAGE: arc study [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
init <init args> Initialize a new empty study file in the arc
register <register args>
Register an existing study in the arc with the given assay metadata.
add <add args> Create a new study file in the arc and subsequently register it with the given study metadata
delete <delete args> Delete a study from the arc file structure
unregister <unregister args>
Unregister a study from the arc investigation file
remove <remove args> Remove a study from the arc
update <update args> Update an existing study in the arc with the given study metadata
edit <edit args> Open and edit an existing study in the arc with a text editor. Arguments passed for this command
will be pre-set in the editor.
show <show args> Show the values of a study
list List all studies registered in the arc
person <person verbs> Person functions
publication <publication verbs>
Publication functions
design <design verbs> Design functions
factor <factor verbs> Factor functions
protocol <protocol verbs>
Protocol functions
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options.USAGE: arc study init [--help] --identifier <study identifier>
OPTIONS:
--identifier <study identifier>
A unique identifier, either a temporary identifier supplied by users or one generated by a
repository or other database. For example, it could be an identifier complying with the LSID
specification.
--help display this list of options.USAGE: arc study register [--help] --identifier <study identifier> [--title <title>] [--description <description>]
[--submissiondate <submission date>] [--publicreleasedate <public release date>]
OPTIONS:
--identifier <study identifier>
A unique identifier, either a temporary identifier supplied by users or one generated by a
repository or other database. For example, it could be an identifier complying with the LSID
specification.
--title <title> A concise phrase used to encapsulate the purpose and goal of the study.
--description <description>
A textual description of the study, with components such as objective or goals.
--submissiondate <submission date>
The date on which the study is submitted to an archive.
--publicreleasedate <public release date>
The date on which the study SHOULD be released publicly.
--help display this list of options.USAGE: arc study add [--help] --identifier <study identifier> [--title <title>] [--description <description>]
[--submissiondate <submission date>] [--publicreleasedate <public release date>]
OPTIONS:
--identifier <study identifier>
A unique identifier, either a temporary identifier supplied by users or one generated by a
repository or other database. For example, it could be an identifier complying with the LSID
specification.
--title <title> A concise phrase used to encapsulate the purpose and goal of the study.
--description <description>
A textual description of the study, with components such as objective or goals.
--submissiondate <submission date>
The date on which the study is submitted to an archive.
--publicreleasedate <public release date>
The date on which the study SHOULD be released publicly.
--help display this list of options.USAGE: arc study delete [--help] --identifier <study identifier>
OPTIONS:
--identifier <study identifier>
A unique identifier, either a temporary identifier supplied by users or one generated by a
repository or other database. For example, it could be an identifier complying with the LSID
specification.
--help display this list of options.USAGE: arc study unregister [--help] --identifier <study identifier>
OPTIONS:
--identifier <study identifier>
A unique identifier, either a temporary identifier supplied by users or one generated by a
repository or other database. For example, it could be an identifier complying with the LSID
specification.
--help display this list of options.USAGE: arc study remove [--help] --identifier <study identifier>
OPTIONS:
--identifier <study identifier>
A unique identifier, either a temporary identifier supplied by users or one generated by a
repository or other database. For example, it could be an identifier complying with the LSID
specification.
--help display this list of options.Give new metadata that overwrite the current metadata of a study.
USAGE: arc study update [--help] --identifier <study identifier> [--title <title>] [--description <description>]
[--submissiondate <submission date>] [--publicreleasedate <public release date>]
OPTIONS:
--identifier <study identifier>
A unique identifier, either a temporary identifier supplied by users or one generated by a
repository or other database. For example, it could be an identifier complying with the LSID
specification.
--title <title> A concise phrase used to encapsulate the purpose and goal of the study.
--description <description>
A textual description of the study, with components such as objective or goals.
--submissiondate <submission date>
The date on which the study is submitted to an archive.
--publicreleasedate <public release date>
The date on which the study SHOULD be released publicly.
--help display this list of options.Take the current metadata of a study and change it.
(While study edit opens the current metadata that can be altered by the user, study update will take a new set of metadata and overwrites the existing one)
USAGE: arc study edit [--help] --identifier <study identifier>
OPTIONS:
--identifier <study identifier>
A unique identifier, either a temporary identifier supplied by users or one generated by a
repository or other database. For example, it could be an identifier complying with the LSID
specification.
--help display this list of options.
USAGE: arc study show [--help] --identifier <study identifier>
OPTIONS:
--identifier <study identifier>
A unique identifier, either a temporary identifier supplied by users or one generated by a
repository or other database. For example, it could be an identifier complying with the LSID
specification.
--help display this list of options.USAGE: arc study person [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
update <update args> Update an existing person in the arc investigation study with the given person metadata. The person
is identified by the full name (first name, last name, mid initials)
edit <edit args> Open and edit an existing person in the arc investigation study with a text editor. The person is
identified by the full name (first name, last name, mid initials)
register <register args>
Register a person in the arc investigation study with the given assay metadata.
unregister <remove args>
Unregister a person from the given investigation study. The person is identified by the full name
(first name, last name, mid initials).
show <show args> Show the metadata of a person registered in the arc investigation study
list List all persons registered in the arc investigation
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options.USAGE: arc study person update [--help] --studyidentifier <string> --lastname <last name> --firstname <first name>
[--midinitials <mid initials>] [--email <e mail>] [--phone <phone number>]
[--fax <fax number>] [--address <adress>] [--affiliation <affiliation>]
[--roles <roles>] [--rolestermaccessionnumber <roles term accession number>]
[--rolestermsourceref <roles term source ref>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the person is associated with
--lastname, -l <last name>
The last name of a person associated with the study.
--firstname, -f <first name>
The first name of a person associated with the study.
--midinitials, -m <mid initials>
The middle initials of a person associated with the study.
--email <e mail> The email address of a person associated with the study.
--phone <phone number>
The telephone number of a person associated with the study.
--fax <fax number> The fax number of a person associated with the study.
--address <adress> The address of a person associated with the study.
--affiliation <affiliation>
The organization affiliation for a person associated with the study.
--roles <roles> Term to classify the role(s) performed by this person in the context of the study, which means that
the roles reported here need not correspond to roles held withing their affiliated organization.
Multiple annotations or values attached to one person can be provided by using a semicolon (";")
Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor) .The term can be free text or
from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term
Accession Number and Term Source REF fields below are required.
--rolestermaccessionnumber <roles term accession number>
The accession number from the Term Source associated with the selected term.
--rolestermsourceref <roles term source ref>
dentifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Names declared in the Ontology Source Reference section.
--help display this list of options.USAGE: arc study person edit [--help] --studyidentifier <string> --lastname <last name> --firstname <first name>
[--midinitials <mid initials>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the person is associated with
--lastname, -l <last name>
The last name of a person associated with the study.
--firstname, -f <first name>
The first name of a person associated with the study.
--midinitials, -m <mid initials>
The middle initials of a person associated with the study.
--help display this list of options.USAGE: arc study person register [--help] --studyidentifier <string> --lastname <last name>
--firstname <first name> [--midinitials <mid initials>] [--email <e mail>]
[--phone <phone number>] [--fax <fax number>] [--address <adress>]
[--affiliation <affiliation>] [--roles <roles>]
[--rolestermaccessionnumber <roles term accession number>]
[--rolestermsourceref <roles term source ref>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the person is associated with
--lastname, -l <last name>
The last name of a person associated with the study.
--firstname, -f <first name>
The first name of a person associated with the study.
--midinitials, -m <mid initials>
The middle initials of a person associated with the study.
--email <e mail> The email address of a person associated with the study.
--phone <phone number>
The telephone number of a person associated with the study.
--fax <fax number> The fax number of a person associated with the study.
--address <adress> The address of a person associated with the study.
--affiliation <affiliation>
The organization affiliation for a person associated with the study.
--roles <roles> Term to classify the role(s) performed by this person in the context of the study, which means that
the roles reported here need not correspond to roles held withing their affiliated organization.
Multiple annotations or values attached to one person can be provided by using a semicolon (";")
Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor) .The term can be free text or
from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term
Accession Number and Term Source REF fields below are required.
--rolestermaccessionnumber <roles term accession number>
The accession number from the Term Source associated with the selected term.
--rolestermsourceref <roles term source ref>
dentifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Names declared in the Ontology Source Reference section.
--help display this list of options.USAGE: arc study person unregister [--help] --studyidentifier <string> --lastname <last name>
--firstname <first name> [--midinitials <mid initials>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the person is associated with
--lastname, -l <last name>
The last name of a person associated with the study.
--firstname, -f <first name>
The first name of a person associated with the study.
--midinitials, -m <mid initials>
The middle initials of a person associated with the study.
--help display this list of options.USAGE: arc study person show [--help] --studyidentifier <string> --lastname <last name> --firstname <first name>
[--midinitials <mid initials>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the person is associated with
--lastname, -l <last name>
The last name of a person associated with the study.
--firstname, -f <first name>
The first name of a person associated with the study.
--midinitials, -m <mid initials>
The middle initials of a person associated with the study.
--help display this list of options.USAGE: arc study publication [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
update <update args> Update an existing publication in the arc investigation study with the given publication metadata.
The publication is identified by the doi
edit <edit args> Open and edit an existing publication in the arc investigation study with a text editor. The
publication is identified by the doi
register <register args>
Register a publication in the arc investigation study with the given assay metadata.
unregister <remove args>
Unregister a publication from the given investigation study. The publication is identified by the doi
show <show args> Show the metadata of a publication registered in the arc investigation study
list List all publication registered in the arc investigation study
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options.USAGE: arc study publication update [--help] --studyidentifier <string> --doi <doi> [--pubmedid <pubmed id>]
[--authorlist <author list>] [--title <publication title>]
[--status <publication status>]
[--statustermaccessionnumber <publication status term accession number>]
[--statustermsourceref <publication status term source ref>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the publication is associated with
--doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available).
--pubmedid, -p <pubmed id>
The PubMed IDs of the described publication(s) associated with this study.
--authorlist <author list>
The list of authors associated with that publication.
--title <publication title>
The title of publication associated with the study.
--status <publication status>
A term describing the status of that publication (i.e. submitted, in preparation, published).
--statustermaccessionnumber <publication status term accession number>
The accession number from the Term Source associated with the selected term.
--statustermsourceref <publication status term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one the Term Source Name declared in the in the Ontology Source Reference section.
--help display this list of options.USAGE: arc study publication edit [--help] --studyidentifier <string> --doi <doi>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the publication is associated with
--doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available).
--help display this list of options.USAGE: arc study publication register [--help] --studyidentifier <string> --doi <doi> [--pubmedid <pubmed id>]
[--authorlist <author list>] [--title <publication title>]
[--status <publication status>]
[--statustermaccessionnumber <publication status term accession number>]
[--statustermsourceref <publication status term source ref>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the publication is associated with
--doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available).
--pubmedid, -p <pubmed id>
The PubMed IDs of the described publication(s) associated with this study.
--authorlist <author list>
The list of authors associated with that publication.
--title <publication title>
The title of publication associated with the study.
--status <publication status>
A term describing the status of that publication (i.e. submitted, in preparation, published).
--statustermaccessionnumber <publication status term accession number>
The accession number from the Term Source associated with the selected term.
--statustermsourceref <publication status term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one the Term Source Name declared in the in the Ontology Source Reference section.
--help display this list of options.USAGE: arc study publication unregister [--help] --studyidentifier <string> --doi <doi>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the publication is associated with
--doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available).
--help display this list of options.USAGE: arc study publication show [--help] --studyidentifier <string> --doi <doi>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the publication is associated with
--doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available).
--help display this list of options.USAGE: arc study design [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
update <update args> Update an existing design in the arc investigation study with the given publication metadata. The
publication is identified by the design type
edit <edit args> Open and edit an existing design in the arc investigation study with a text editor. The publication
is identified by the design type
register <register args>
Register a design in the arc investigation study with the given assay metadata.
unregister <remove args>
Unregister a design from the given investigation study. The publication is identified by the design
type
show <show args> Show the metadata of a design registered in the arc investigation study
list List all design registered in the arc investigation study
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options.USAGE: arc study design update [--help] --studyidentifier <string> --designtype <design type>
[--typetermaccessionnumber <type term accession number>]
[--typetermsourceref <type term source ref>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--designtype, -d <design type>
A term allowing the classification of the study based on the overall experimental design, e.g
cross-over design or parallel group design. The term can be free text or from, for example, a
controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and
Term Source REF fields below are required.
--typetermaccessionnumber <type term accession number>
The accession number from the Term Source associated with the selected term.
--typetermsourceref <type term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Study Design Term
Source REF has to match one the Term Source Name declared in the Ontology Source Reference section.
--help display this list of options.USAGE: arc study design edit [--help] --studyidentifier <string> --designtype <design type>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--designtype, -d <design type>
A term allowing the classification of the study based on the overall experimental design, e.g
cross-over design or parallel group design. The term can be free text or from, for example, a
controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and
Term Source REF fields below are required.
--help display this list of options.USAGE: arc study design register [--help] --studyidentifier <string> --designtype <design type>
[--typetermaccessionnumber <type term accession number>]
[--typetermsourceref <type term source ref>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--designtype, -d <design type>
A term allowing the classification of the study based on the overall experimental design, e.g
cross-over design or parallel group design. The term can be free text or from, for example, a
controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and
Term Source REF fields below are required.
--typetermaccessionnumber <type term accession number>
The accession number from the Term Source associated with the selected term.
--typetermsourceref <type term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Study Design Term
Source REF has to match one the Term Source Name declared in the Ontology Source Reference section.
--help display this list of options.USAGE: arc study design unregister [--help] --studyidentifier <string> --designtype <design type>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--designtype, -d <design type>
A term allowing the classification of the study based on the overall experimental design, e.g
cross-over design or parallel group design. The term can be free text or from, for example, a
controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and
Term Source REF fields below are required.
--help display this list of options.USAGE: arc study design show [--help] --studyidentifier <string> --designtype <design type>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--designtype, -d <design type>
A term allowing the classification of the study based on the overall experimental design, e.g
cross-over design or parallel group design. The term can be free text or from, for example, a
controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and
Term Source REF fields below are required.
--help display this list of options.USAGE: arc study factor [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
update <update args> Update an existing factor in the arc investigation study with the given publication metadata. The
publication is identified by name
edit <edit args> Open and edit an existing factor in the arc investigation study with a text editor. The publication
is identified by name
register <register args>
Register a factor in the arc investigation study with the given assay metadata.
unregister <remove args>
Unregister a factor from the given investigation study. The publication is identified by name
show <show args> Show the metadata of a factor registered in the arc investigation study
list List all factor registered in the arc investigation study
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options.USAGE: arc study factor update [--help] --studyidentifier <string> --name <name> [--factortype <factor type>]
[--typetermaccessionnumber <type term accession number>]
[--typetermsourceref <type term source ref>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent
variable manipulated by the experimentalist with the intention to affect biological systems in a way
that can be measured by an assay. The value of a factor is given in the Study or Assay file,
accordingly. If both Study and Assay have a Factor Value, these must be different.
--factortype <factor type>
A term allowing the classification of this factor into categories. The term can be free text or
from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term
Accession Number and Term Source REF fields below are required.
--typetermaccessionnumber <type term accession number>
The accession number from the Term Source associated with the selected term.
--typetermsourceref <type term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Name declared in the Ontology Source Reference section.
--help display this list of options.USAGE: arc study factor edit [--help] --studyidentifier <string> --name <name>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent
variable manipulated by the experimentalist with the intention to affect biological systems in a way
that can be measured by an assay. The value of a factor is given in the Study or Assay file,
accordingly. If both Study and Assay have a Factor Value, these must be different.
--help display this list of options.USAGE: arc study factor register [--help] --studyidentifier <string> --name <name> [--factortype <factor type>]
[--typetermaccessionnumber <type term accession number>]
[--typetermsourceref <type term source ref>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent
variable manipulated by the experimentalist with the intention to affect biological systems in a way
that can be measured by an assay. The value of a factor is given in the Study or Assay file,
accordingly. If both Study and Assay have a Factor Value, these must be different.
--factortype <factor type>
A term allowing the classification of this factor into categories. The term can be free text or
from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term
Accession Number and Term Source REF fields below are required.
--typetermaccessionnumber <type term accession number>
The accession number from the Term Source associated with the selected term.
--typetermsourceref <type term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Name declared in the Ontology Source Reference section.
--help display this list of options.USAGE: arc study factor unregister [--help] --studyidentifier <string> --name <name>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent
variable manipulated by the experimentalist with the intention to affect biological systems in a way
that can be measured by an assay. The value of a factor is given in the Study or Assay file,
accordingly. If both Study and Assay have a Factor Value, these must be different.
--help display this list of options.USAGE: arc study factor show [--help] --studyidentifier <string> --name <name>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent
variable manipulated by the experimentalist with the intention to affect biological systems in a way
that can be measured by an assay. The value of a factor is given in the Study or Assay file,
accordingly. If both Study and Assay have a Factor Value, these must be different.
--help display this list of options.USAGE: arc study protocol [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
update <update args> Update an existing protocol in the arc investigation study with the given publication metadata. The
publication is identified by name
edit <edit args> Open and edit an existing protocol in the arc investigation study with a text editor. The
publication is identified by name
register <register args>
Register a protocol in the arc investigation study with the given assay metadata.
unregister <remove args>
Unregister a protocol from the given investigation study. The publication is identified by name
show <show args> Show the metadata of a protocol registered in the arc investigation study
list List all protocol registered in the arc investigation study
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options.USAGE: arc study protocol update [--help] --studyidentifier <string> --name <name>
[--protocoltype <protocol type>]
[--typetermaccessionnumber <type term accession number>]
[--typetermsourceref <type term source ref>] [--description <description>]
[--uri <uri>] [--version <version>] [--parametersname <parameters name>]
[--parameterstermaccessionnumber <parameters term accession number>]
[--parameterstermsourceref <parameters term source ref>]
[--componentsname <compoments name>] [--componentstype <compoments type>]
[--componentstypetermaccessionnumber <compoments type accession number>]
[--componentstypetermsourceref <compoments type term source ref>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--name, -n <name> The name of the protocols used within the ISA-Tab document. The names are used as identifiers within
the ISA-Tab document and will be referenced in the Study and Assay files in the Protocol REF
columns. Names can be either local identifiers, unique within the ISA Archive which contains them,
or fully qualified external accession numbers.
--protocoltype <protocol type>
Term to classify the protocol. The term can be free text or from, for example, a controlled
vocabulary or an ontology. If the latter source is used the Term Accession Number and Term Source
REF fields below are required.
--typetermaccessionnumber <type term accession number>
The accession number from the Term Source associated with the selected term.
--typetermsourceref <type term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Name declared in the Ontology Source Reference section.
--description <description>
A free-text description of the protocol.
--uri <uri> Pointer to protocol resources external to the ISA-Tab that can be accessed by their Uniform Resource
Identifier (URI).
--version <version> An identifier for the version to ensure protocol tracking.
--parametersname <parameters name>
A semicolon-delimited (";") list of parameter names, used as an identifier within the ISA-Tab
document. These names are used in the Study and Assay files (in the "Parameter Value []" column
heading) to list the values used for each protocol parameter. Refer to section Multiple values
fields in the Investigation File on how to encode multiple values in one field and match term sources
--parameterstermaccessionnumber <parameters term accession number>
The accession number from the Term Source associated with the selected term.
--parameterstermsourceref <parameters term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Name declared in the Ontology Source Reference section.
--componentsname <compoments name>
A semicolon-delimited (";") list of a protocol's components; e.g. instrument names, software names,
and reagents names. Refer to section Multiple values fields in the Investigation File on how to
encode multiple components in one field and match term sources.
--componentstype <compoments type>
Term to classify the protocol components listed for example, instrument, software, detector or
reagent. The term can be free text or from, for example, a controlled vocabulary or an ontology. If
the latter source is used the Term Accession Number and Term Source REF fields below are required.
--componentstypetermaccessionnumber <compoments type accession number>
The accession number from the Source associated to the selected terms.
--componentstypetermsourceref <compoments type term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match a Term Source Name previously declared in the ontology section.
--help display this list of options.USAGE: arc study protocol edit [--help] --studyidentifier <string> --name <name>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent
variable manipulated by the experimentalist with the intention to affect biological systems in a way
that can be measured by an assay. The value of a factor is given in the Study or Assay file,
accordingly. If both Study and Assay have a Factor Value, these must be different.
--help display this list of options.USAGE: arc study protocol register [--help] --studyidentifier <string> --name <name>
[--protocoltype <protocol type>]
[--typetermaccessionnumber <type term accession number>]
[--typetermsourceref <type term source ref>] [--description <description>]
[--uri <uri>] [--version <version>] [--parametersname <parameters name>]
[--parameterstermaccessionnumber <parameters term accession number>]
[--parameterstermsourceref <parameters term source ref>]
[--componentsname <compoments name>] [--componentstype <compoments type>]
[--componentstypetermaccessionnumber <compoments type accession number>]
[--componentstypetermsourceref <compoments type term source ref>]
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--name, -n <name> The name of the protocols used within the ISA-Tab document. The names are used as identifiers within
the ISA-Tab document and will be referenced in the Study and Assay files in the Protocol REF
columns. Names can be either local identifiers, unique within the ISA Archive which contains them,
or fully qualified external accession numbers.
--protocoltype <protocol type>
Term to classify the protocol. The term can be free text or from, for example, a controlled
vocabulary or an ontology. If the latter source is used the Term Accession Number and Term Source
REF fields below are required.
--typetermaccessionnumber <type term accession number>
The accession number from the Term Source associated with the selected term.
--typetermsourceref <type term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Name declared in the Ontology Source Reference section.
--description <description>
A free-text description of the protocol.
--uri <uri> Pointer to protocol resources external to the ISA-Tab that can be accessed by their Uniform Resource
Identifier (URI).
--version <version> An identifier for the version to ensure protocol tracking.
--parametersname <parameters name>
A semicolon-delimited (";") list of parameter names, used as an identifier within the ISA-Tab
document. These names are used in the Study and Assay files (in the "Parameter Value []" column
heading) to list the values used for each protocol parameter. Refer to section Multiple values
fields in the Investigation File on how to encode multiple values in one field and match term sources
--parameterstermaccessionnumber <parameters term accession number>
The accession number from the Term Source associated with the selected term.
--parameterstermsourceref <parameters term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Name declared in the Ontology Source Reference section.
--componentsname <compoments name>
A semicolon-delimited (";") list of a protocol's components; e.g. instrument names, software names,
and reagents names. Refer to section Multiple values fields in the Investigation File on how to
encode multiple components in one field and match term sources.
--componentstype <compoments type>
Term to classify the protocol components listed for example, instrument, software, detector or
reagent. The term can be free text or from, for example, a controlled vocabulary or an ontology. If
the latter source is used the Term Accession Number and Term Source REF fields below are required.
--componentstypetermaccessionnumber <compoments type accession number>
The accession number from the Source associated to the selected terms.
--componentstypetermsourceref <compoments type term source ref>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match a Term Source Name previously declared in the ontology section.
--help display this list of options.USAGE: arc study protocol unregister [--help] --studyidentifier <string> --name <name>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent
variable manipulated by the experimentalist with the intention to affect biological systems in a way
that can be measured by an assay. The value of a factor is given in the Study or Assay file,
accordingly. If both Study and Assay have a Factor Value, these must be different.
--help display this list of options.USAGE: arc study protocol show [--help] --studyidentifier <string> --name <name>
OPTIONS:
--studyidentifier, -s <string>
Identifier of the study the design is associated with
--name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent
variable manipulated by the experimentalist with the intention to affect biological systems in a way
that can be measured by an assay. The value of a factor is given in the Study or Assay file,
accordingly. If both Study and Assay have a Factor Value, these must be different.
--help display this list of options.USAGE: arc assay [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
init <init args> Initialize a new empty assay and associated folder structure in the arc.
register <register args>
Register an existing assay in the arc with the given assay metadata.
add <add args> Create a new assay file and associated folder structure in the arc and subsequently register it with
the given assay metadata
delete <delete args> Delete the given assays folder and its underlying file structure
unregister <unregister args>
Unregister an assay from the given studys' assay register in the investigation file
remove <remove args> Both unregister and assay from the investigation file and delete its folders and files
update <update args> Update an existing assay in the arc with the given assay metadata
edit <edit args> Open and edit an existing assay in the arc with a text editor. Arguments passed for this command
will be pre-set in the editor.
move <move args> Move an assay from one study to another
show <show args> Show the values of an existing assay
list List all assays registered in the arc
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options.USAGE: arc assay init [--help] --assayidentifier <assay identifier>
OPTIONS:
--assayidentifier, -a <assay identifier>
Identifier of the assay, will be used as name of the root folder of the new assay folder structure
--help display this list of options.USAGE: arc assay register [--help] [--studyidentifier <string>] --assayidentifier <string>
[--measurementtype <measurement type>]
[--measurementtypetermaccessionnumber <measurement type accession>]
[--measurementtypetermsourceref <measurement type term source>]
[--technologytype <technology type>]
[--technologytypetermaccessionnumber <technology type accession>]
[--technologytypetermsourceref <technology type term source>]
[--technologyplatform <technology platform>]
OPTIONS:
--studyidentifier, -s <string>
Name of the study in which the assay is situated
--assayidentifier, -a <string>
Name of the assay of interest
--measurementtype <measurement type>
A term to qualify the endpoint, or what is being measured (e.g. gene expression profiling or protein
identification). The term can be free text or from, for example, a controlled vocabulary or an
ontology. If the latter source is used the Term Accession Number and Term Source REF fields below
are required.
--measurementtypetermaccessionnumber <measurement type accession>
The accession number from the Term Source associated with the selected term.
--measurementtypetermsourceref <measurement type term source>
The Source REF has to match one of the Term Source Name declared in the Ontology Source Reference
section.
--technologytype <technology type>
Term to identify the technology used to perform the measurement, e.g. DNA microarray, mass
spectrometry. The term can be free text or from, for example, a controlled vocabulary or an
ontology. If the latter source is used the Term Accession Number and Term Source REF fields below
are required.
--technologytypetermaccessionnumber <technology type accession>
The accession number from the Term Source associated with the selected term.
--technologytypetermsourceref <technology type term source>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Names declared in the Ontology Source Reference section.
--technologyplatform <technology platform>
Manufacturer and platform name, e.g. Bruker AVANCE
--help display this list of options.USAGE: arc assay add [--help] [--studyidentifier <string>] --assayidentifier <string>
[--measurementtype <measurement type>]
[--measurementtypetermaccessionnumber <measurement type accession>]
[--measurementtypetermsourceref <measurement type term source>]
[--technologytype <technology type>]
[--technologytypetermaccessionnumber <technology type accession>]
[--technologytypetermsourceref <technology type term source>]
[--technologyplatform <technology platform>]
OPTIONS:
--studyidentifier, -s <string>
Name of the study in which the assay is situated
--assayidentifier, -a <string>
Name of the assay of interest
--measurementtype <measurement type>
A term to qualify the endpoint, or what is being measured (e.g. gene expression profiling or protein
identification). The term can be free text or from, for example, a controlled vocabulary or an
ontology. If the latter source is used the Term Accession Number and Term Source REF fields below
are required.
--measurementtypetermaccessionnumber <measurement type accession>
The accession number from the Term Source associated with the selected term.
--measurementtypetermsourceref <measurement type term source>
The Source REF has to match one of the Term Source Name declared in the Ontology Source Reference
section.
--technologytype <technology type>
Term to identify the technology used to perform the measurement, e.g. DNA microarray, mass
spectrometry. The term can be free text or from, for example, a controlled vocabulary or an
ontology. If the latter source is used the Term Accession Number and Term Source REF fields below
are required.
--technologytypetermaccessionnumber <technology type accession>
The accession number from the Term Source associated with the selected term.
--technologytypetermsourceref <technology type term source>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Names declared in the Ontology Source Reference section.
--technologyplatform <technology platform>
Manufacturer and platform name, e.g. Bruker AVANCE
--help display this list of options.USAGE: arc assay delete [--help] --assayidentifier <assay identifier>
OPTIONS:
--assayidentifier, -a <assay identifier>
Identifier of the assay, will be used as name of the root folder of the new assay folder structure
--help display this list of options.USAGE: arc assay unregister [--help] [--studyidentifier <study identifier>] --assayidentifier <assay identifier>
OPTIONS:
--studyidentifier, -s <study identifier>
Identifier of the study in which the assay is registered
--assayidentifier, -a <assay identifier>
Identifier of the assay of interest
--help display this list of options.USAGE: arc assay remove [--help] [--studyidentifier <study identifier>] --assayidentifier <assay identifier>
OPTIONS:
--studyidentifier, -s <study identifier>
Identifier of the study in which the assay is registered
--assayidentifier, -a <assay identifier>
Identifier of the assay of interest
--help display this list of options.Give new metadata that overwrite the current metadata of an assay.
USAGE: arc assay update [--help] [--studyidentifier <string>] --assayidentifier <string>
[--measurementtype <measurement type>]
[--measurementtypetermaccessionnumber <measurement type accession>]
[--measurementtypetermsourceref <measurement type term source>]
[--technologytype <technology type>]
[--technologytypetermaccessionnumber <technology type accession>]
[--technologytypetermsourceref <technology type term source>]
[--technologyplatform <technology platform>]
OPTIONS:
--studyidentifier, -s <string>
Name of the study in which the assay is situated
--assayidentifier, -a <string>
Name of the assay of interest
--measurementtype <measurement type>
A term to qualify the endpoint, or what is being measured (e.g. gene expression profiling or protein
identification). The term can be free text or from, for example, a controlled vocabulary or an
ontology. If the latter source is used the Term Accession Number and Term Source REF fields below
are required.
--measurementtypetermaccessionnumber <measurement type accession>
The accession number from the Term Source associated with the selected term.
--measurementtypetermsourceref <measurement type term source>
The Source REF has to match one of the Term Source Name declared in the Ontology Source Reference
section.
--technologytype <technology type>
Term to identify the technology used to perform the measurement, e.g. DNA microarray, mass
spectrometry. The term can be free text or from, for example, a controlled vocabulary or an
ontology. If the latter source is used the Term Accession Number and Term Source REF fields below
are required.
--technologytypetermaccessionnumber <technology type accession>
The accession number from the Term Source associated with the selected term.
--technologytypetermsourceref <technology type term source>
Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to
match one of the Term Source Names declared in the Ontology Source Reference section.
--technologyplatform <technology platform>
Manufacturer and platform name, e.g. Bruker AVANCE
--help display this list of options.Take the current metadata of an assay and change it.
(While assay edit opens the current metadata that can be altered by the user, assay update will take a new set of metadata and overwrites the existing one)
USAGE: arc assay edit [--help] [--studyidentifier <study identifier>] --assayidentifier <assay identifier>
OPTIONS:
--studyidentifier, -s <study identifier>
Identifier of the study in which the assay is registered
--assayidentifier, -a <assay identifier>
Identifier of the assay of interest
--help display this list of options.USAGE: arc assay move [--help] --studyidentifier <study identifier> --assayidentifier <assay identifier>
--targetstudyidentifier <target study identifier>
OPTIONS:
--studyidentifier, -s <study identifier>
Name of the study in which the assay is situated
--assayidentifier, -a <assay identifier>
Name of the assay of interest
--targetstudyidentifier, -t <target study identifier>
Target study to which the assay should be moved
--help display this list of options.USAGE: arc assay show [--help] [--studyidentifier <study identifier>] --assayidentifier <assay identifier>
OPTIONS:
--studyidentifier, -s <study identifier>
Identifier of the study in which the assay is registered
--assayidentifier, -a <assay identifier>
Identifier of the assay of interest
--help display this list of options.USAGE: arc configuration [--help] [<subcommand> [<options>]]
SUBCOMMANDS:
edit <edit args> Open and edit an existing assay in the arc with a text editor. Arguments passed for this command
will be pre-set in the editor.
list <list args> List all assays registered in the arc.
set <set args> Assign the given value to the given name.
unset <unset args> Remove the value bound to the given name.
Use 'arc <subcommand> --help' for additional information.
OPTIONS:
--help display this list of options.USAGE: arc configuration list [--help] [--local] [--global]
OPTIONS:
--local, -l Lists the local settings for this arc
--global, -g Lists the global settings of the arccommander
--help display this list of options.USAGE: arc configuration edit [--help] [--local] [--global]
OPTIONS:
--local, -l Edit the local settings for this arc
--global, -g Edit the global settings of the arccommander
--help display this list of options.USAGE: arc configuration set [--help] [--local] [--global] --name <string> --value <string>
OPTIONS:
--local, -l Set the the value of the name locally for this arc
--global, -g Set the the value of the name globally for the arccommander
--name, -n <string> The name of the setting in 'Section.Key' format
--value, -v <string> The new value of the setting
--help display this list of options.USAGE: arc configuration unset [--help] [--local] [--global] --name <string>
OPTIONS:
--local, -l Unset the the value of the name locally for this arc
--global, -g Unset the the value of the name globally for the arccommander
--name, -n <string> The name of the setting in 'Section.Key' format
--help display this list of options.Content
- Before we start
- ARC initialization
-
Investigation
3.1 Addition of an isa.investigation.xlsx
3.2 Registering persons to investigation
3.2.1 Listing and inspecting registered persons
3.2.2 Editing person information
3.2.3 Removing a person
3.3 Registering publications to investigation
3.3.1 Listing and inspecting registered publications
3.3.2 Editing publication information
3.3.3 Removing a publication -
Study
4.1 Addition of studies
4.2 Listing and inspecting registered studies
4.3 Editing study information
4.4 Removing studies
4.5 Registering persons to studies
4.5.1 Listing and inspecting registered persons
4.5.2 Editing person information
4.5.3 Removing a person
4.6 Registering publications to studies
4.6.1 Listing and inspecting registered publications
4.6.2 Editing publication information
4.6.3 Removing a publication -
Assay
5.1 Addition of assays
5.2 Listing and inspecting registered assays
5.3 Editing assay information
5.4 Removing assays
5.5 Moving assays -
ARC Synchronization
6.1 Working on a second branch
6.2 Setting a git user