diff GEMBASSY-1.0.3/acd/gbaserelativeentropy.acd @ 2:8947fca5f715 draft default tip

Uploaded

--- a/GEMBASSY-1.0.3/acd/gbaserelativeentropy.acd	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-application: gbaserelativeentropy [
-  documentation: "Calculates and graphs the sequence conservation using
-                  Kullback-Leibler divergence (relative entropy)"
-  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: 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"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "gbaserelativeentropy 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