GCModeller [version 1.0.2.3]

Module AssemblyName: file:///G:/GCModeller/manual/bin/GCModeller.exe
Root namespace: xGCModeller.CLI

All of the command that available in this program has been list below:

Function API Info
/Draw.Comparative
/Export.Basys
/init.manuals
/Install.genbank
/Located.AppData
/Visual.BBH
–Drawing.ChromosomeMap Drawing the chromosomes map from the PTT object as the basically genome information source.
–Drawing.ClustalW
export Export the calculation data from a specific data table in the mysql database server.
–Gendist.From.Self.Overviews
–Gendist.From.SelfMPAlignment
–Get.Subset.lstID
help Show help information about this program.
-imports
–install.MYSQL
–install-CDD
–install-COGs Install the COGs database into the GCModeller database.
–Interpro.Build
–ls Listing all of the available GCModeller CLI tools commands.
–user.create

Commands


Help for command ‘/Draw.Comparative’:

Prototype: xGCModeller.CLI::Int32 DrawMultipleAlignments(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe /Draw.Comparative /in <meta.Xml> /PTT <PTT_DIR> [/out <outDIR>]
Example: GCModeller /Draw.Comparative
Help for command ‘/Export.Basys’:

Prototype: xGCModeller.CLI::Int32 ExportBaSys(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe /Export.Basys /in <in.DIR> [/out <out.DIR>]
Example: GCModeller /Export.Basys
Help for command ‘/init.manuals’:

Prototype: xGCModeller.CLI::Int32 InitManuals(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe /init.manuals
Example: GCModeller /init.manuals
Help for command ‘/Install.genbank’:

Prototype: xGCModeller.CLI::Int32 InstallGenbank(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe /Install.genbank /imports <all_genbanks.DIR> [/refresh]
Example: GCModeller /Install.genbank
Help for command ‘/Located.AppData’:

Prototype: xGCModeller.CLI::Int32 LocatedAppData(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe
Example: GCModeller /Located.AppData
Help for command ‘/Visual.BBH’:

Prototype: xGCModeller.CLI::Int32 BBHVisual(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe /Visual.BBH /in <bbh.Xml> /PTT <genome.PTT> /density <genomes.density.DIR> [/limits <sp-list.txt> /out <image.png>]
Example: GCModeller /Visual.BBH

Parameters information:

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/PTT
Description: A directory which contains all of the information data files for the reference genome,
this directory would includes *.gb, *.ptt, *.gff, *.fna, *.faa, etc.

Example: /PTT ""

Accepted Types

/PTT
Help for command ‘–Drawing.ChromosomeMap’:

Prototype: xGCModeller.CLI::Int32 DrawingChrMap(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Drawing the chromosomes map from the PTT object as the basically genome information source.
Usage: G:\GCModeller\manual\bin\GCModeller.exe --Drawing.ChromosomeMap /ptt <genome.ptt> [/conf <config.inf> /out <dir.export> /COG <cog.csv>]
Example: GCModeller --Drawing.ChromosomeMap
Help for command ‘–Drawing.ClustalW’:

Prototype: xGCModeller.CLI::Int32 DrawClustalW(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe --Drawing.ClustalW /in <align.fasta> [/out <out.png> /dot.Size 10]
Example: GCModeller --Drawing.ClustalW
Help for command ‘export’:

Prototype: xGCModeller.CLI::Int32 ExportData(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Export the calculation data from a specific data table in the mysql database server.
Usage: G:\GCModeller\manual\bin\GCModeller.exe export -mysql <mysql_connection_string> [-o <output_save_file/dir> -t <table_name>]
Example: GCModeller export export -t all -o ~/Desktop/ -mysql "http://localhost:8080/client?user=username%password=password%database=database"

Parameters information:

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    -mysql
Description: The mysql connection string for gc program connect to a specific mysql database server.

Example: -mysql "http://localhost:8080/client?user=username%password=password%database=database"

[-t]
Description: Optional, The target table name for export the data set, there is a option value for this switch: all.
<name> - export the data in the specific name of the table;
all - Default, export all of the table in the database, and at the mean time the -o switch value will be stand for the output directory of the exported csv files.

Example: -t "all"

[-o]
Description: Optional, The path of the export csv file save, it can be a directory or a file path, depend on the value of the -t switch value.
Default is desktop directory and table name combination

Example: -o "~/Desktop/"

Accepted Types

-mysql
-t
-o
Help for command ‘–Gendist.From.Self.Overviews’:

Prototype: xGCModeller.CLI::Int32 SelfOverviewAsMAT(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe --Gendist.From.Self.Overviews /blast_out <blast_out.txt>
Example: GCModeller --Gendist.From.Self.Overviews
Help for command ‘–Gendist.From.SelfMPAlignment’:

Prototype: xGCModeller.CLI::Int32 SelfMPAlignmentAsMAT(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe --Gendist.From.SelfMPAlignment /aln <mpalignment.csv>
Example: GCModeller --Gendist.From.SelfMPAlignment
Help for command ‘–Get.Subset.lstID’:

Prototype: xGCModeller.CLI::Int32 GetSubsetID(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe --Get.Subset.lstID /subset <lstID.txt> /lstID <lstID.csv>
Example: GCModeller --Get.Subset.lstID
Help for command ‘help’:

Prototype: xGCModeller.CLI::Int32 About()

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Information:  Show help information about this program.
Usage: G:\GCModeller\manual\bin\GCModeller.exe gc help
Example: GCModeller help gc help
Help for command ‘-imports’:

Prototype: xGCModeller.CLI::Int32 Imports(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe -imports <genbank_file/genbank_directory>
Example: GCModeller -imports
Help for command ‘–install.MYSQL’:

Prototype: xGCModeller.CLI::Int32 InstallMySQL(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe --install.MYSQL /user <userName> /pass <password> /repository <host_ipAddress> [/port 3306 /database <GCModeller>]
Example: GCModeller --install.MYSQL
Help for command ‘–install-CDD’:

Prototype: xGCModeller.CLI::Int32 InstallCDD(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe --install-CDD /cdd <cdd.DIR>
Example: GCModeller --install-CDD
Help for command ‘–install-COGs’:

Prototype: xGCModeller.CLI::Int32 InstallCOGs(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Install the COGs database into the GCModeller database.
Usage: G:\GCModeller\manual\bin\GCModeller.exe --install-COGs /COGs <Dir.COGs>
Example: GCModeller --install-COGs
Help for command ‘–Interpro.Build’:

Prototype: xGCModeller.CLI::Int32 BuildFamilies(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe --Interpro.Build /xml <interpro.xml>
Example: GCModeller --Interpro.Build
Help for command ‘–ls’:

Prototype: xGCModeller.CLI::Int32 List(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Listing all of the available GCModeller CLI tools commands.
Usage: G:\GCModeller\manual\bin\GCModeller.exe
Example: GCModeller --ls
Help for command ‘–user.create’:

Prototype: xGCModeller.CLI::Int32 Register(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\GCModeller.exe
Example: GCModeller --user.create