Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/acd/gcai.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/gcai.acd Fri Jun 26 05:19:29 2015 -0400 @@ -0,0 +1,64 @@ +application: gcai [ + documentation: "Calculates codon adaptation index for each gene" + groups: "Nucleic:Codon usage" + embassy: "gembassy" + relations: "EDAM_operation:0286 Codon usage analysis" + relations: "EDAM_topic:0107 Codon usage analysis" +] + +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" +] + + boolean: translate [ + information: "Include when translating using standard codon table" + default: "N" + ] + + string: wabsent [ + information: "W value of codons absent from a reference set to negative + when excludes such codons from the calculation" + + default: "-1" + ] + + boolean: tai [ + information: "Include when calculating tRNA adaptation index (TAI)" + default: "N" + ] + + 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: "Codon usage output file" + knowntype: "codon usage" + relations: "EDAM_data:2865 Codon usage bias" + ] + +endsection: output