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

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/acd/gbaseinformationcontent.acd	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,84 @@
+application: gbaseinformationcontent [
+  documentation: "Calculates and graphs the sequence conservation using
+                  information content"
+  groups: "Nucleic:Composition"
+  embassy: "gembassy"
+  relations: "EDAM_topic:0160 Sequence sites and features"
+  relations: "EDAM_operation:0253 Feature prediction"
+]
+
+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: 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"
+  ]
+
+  integer: patlen [
+    information: "Length of oligomer to count"
+    default: "3"
+  ]
+
+  boolean: accid [
+    information: "Include to use sequence accession ID as query"
+    default: "N"
+  ]
+
+endsection: advanced
+
+section: output [
+  information: "Output section"
+  type: "page"
+]
+
+  toggle: plot [
+    information: "Include to plot result"
+    default: "Y"
+  ]
+
+  xygraph: graph [
+    standard: "$(plot)"
+    gtitle: "gbaseinformationcontent of $(sequence.name)"
+    relations: "EDAM_data:2166 Sequence compisition plot"
+  ]
+
+  outfile: outfile [
+    standard: "@(!$(plot))"
+    nullok: "Y"
+    nulldefault: "$(plot)"
+    information: "Program compseq output file (optional)"
+    knowntype: "compseq output"
+    relations: "EDAM_data:3086 Nucleic acid sequence composition"
+  ]
+
+endsection: output
+