Circos - SMRUCC/GCModeller GitHub Wiki

title: Circos tags: [maunal, tools] date: 7/27/2016 6:40:15 PM

GCModeller [version 1.0.0.0]

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

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

Function API Info
/Alignment.Dumps
/DOOR.COGs
/MGA2Myva
/NT.Variation
/Regulons.Dumps
--AT.Percent
--GC.Skew

Commands

Help for command '/Alignment.Dumps':

Prototype: Circos_CLITools.CLI::Int32 AlignmentTableDump(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Circos.exe /Alignment.Dumps /in <inDIR> [/out <out.Xml>]
  Example:      Circos /Alignment.Dumps
Help for command '/DOOR.COGs':

Prototype: Circos_CLITools.CLI::Int32 DOOR_COGs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Circos.exe /DOOR.COGs /DOOR <genome.opr> [/out <out.COGs.Csv>]
  Example:      Circos /DOOR.COGs
Help for command '/MGA2Myva':

Prototype: Circos_CLITools.CLI::Int32 MGA2Myva(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Circos.exe /MGA2Myva /in <mga_cog.csv> [/out <myva_cog.csv> /map <genome.gb>]
  Example:      Circos /MGA2Myva
Help for command '/NT.Variation':

Prototype: Circos_CLITools.CLI::Int32 NTVariation(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Circos.exe /NT.Variation /mla <fasta.fa> [/ref <index/fasta.fa, 0> /out <out.txt> /cut 0.75]
  Example:      Circos /NT.Variation
Help for command '/Regulons.Dumps':

Prototype: Circos_CLITools.CLI::Int32 DumpNames(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Circos.exe /Regulons.Dumps /in <genomes.bbh.DIR> /ptt <genome.ptt> [/out <out.Csv>]
  Example:      Circos /Regulons.Dumps
Help for command '--AT.Percent':

Prototype: Circos_CLITools.CLI::Int32 ATContent(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Circos.exe --AT.Percent /in <in.fasta> [/win_size <200> /step <25> /out <out.txt>]
  Example:      Circos --AT.Percent
Help for command '--GC.Skew':

Prototype: Circos_CLITools.CLI::Int32 GCSkew(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Circos.exe --GC.Skew /in <in.fasta> [/win_size <200> /step <25> /out <out.txt>]
  Example:      Circos --GC.Skew

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