diff GEMBASSY-1.0.3/acd/gdinuc.acd @ 0:8300eb051bea draft

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/acd/gdinuc.acd	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,68 @@
+application: gdinuc [
+  documentation: "Calculates dinucleotide usage "
+  groups: "Nucleic:Codon Usage"
+  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"
+]
+
+  boolean: translate [
+    information: "Include when translates using standard codon table"
+    default: "N"
+  ]
+
+  list: position [
+    information: "Codon position or reading frame"
+    values: "all:Assess all codon positions;
+             12:Assess the reading frame 1-2;
+             23:Assess the reading frame 2-3;
+             31:Assess the reading frame 3-1"
+    default: "all"
+  ]
+
+  string: delkey [
+    information: "Regular expression to delete key (i.e. amino acids and nucleotides)"
+    knowntype: "regular expression"
+    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
+  ]
+
+  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: "Program compseq output file"
+    knowntype: "compseq output"
+    relations: "EDAM_data:3086 Nucleic acid sequence composition"
+  ]
+
+endsection: output