Mercurial > repos > ktnyt > gembassy
view GEMBASSY-1.0.3/acd/gbasecounter.acd @ 0:8300eb051bea draft
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:19:29 -0400 |
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application: gbasecounter [ documentation: "Creates a position weight matrix of oligomers around start codon" groups: "Nucleic:Composition" embassy: "gembassy" relations: "EDAM_topic:0157 Sequence composition analysis" relations: "EDAM_operation:0377 Sequence composition calculation (nucleic acid)" ] section: input [ information: "Input section" type: "page" ] seqall: sequence [ parameter: "Y" type: "nucleotide" features: "Y" relations: "EDAM_data:0849 Sequence record" ] endsection: input section: advanced [ information: "Advanced section" type: "page" ] selection: position [ information: "Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM" values: "start;end" default: "start" ] integer: patlen [ information: "Length of oligomer to count" default: "3" ] integer: upstream [ information: "Length upstream of specified position to create PWM" default: "30" ] integer: downstream [ information: "Length downstream of specified position to create PWM" default: "30" ] boolean: accid [ information: "Include to use sequence accession ID as query" default: "N" ] endsection: advanced section: output [ information: "Output section" type: "page" ] outfile: outfile [ parameter: "Y" information: "Weight matrix output file" knowntype: "matrix" relations: "EDAM_data:1362 Position weight matrix" ] endsection: output