Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/acd/gbasecounter.acd @ 0:8300eb051bea draft
Initial upload
author | ktnyt |
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date | Fri, 26 Jun 2015 05:19:29 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEMBASSY-1.0.3/acd/gbasecounter.acd Fri Jun 26 05:19:29 2015 -0400 @@ -0,0 +1,71 @@ +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