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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2012-06-22 10:03:24 UTC
  • mfrom: (1.1.3)
  • Revision ID: package-import@ubuntu.com-20120622100324-v9e98arr9zjtmitl
Tags: 1:0.1.0+20110714-1
* New upstream version
* debian/control:
   - Standards-Version: 3.9.3 (no changes needed)
   - debhelper version 9
   - Adapted versioned (build-)depends to latest emboss version
* added debian/compat: 9
* debian/source/format: 3.0 (quilt)
* debian/rules: short dh
* debian/copyright: DEP5 fixes

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emboss_acd/seqsearch.acd
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application: seqsearch [
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  documentation: "Generate PSI-BLAST hits (DHF file) from a
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                  DAF file."
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  groups: "Protein:3D Structure"
 
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  groups: "Protein:Profiles"
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  gui: "yes"
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  batch: "yes"
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  cpu: "medium"
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  embassy: "domsearch"
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  external: "blastpgp NCBI toolkit or blast executables"
 
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  relations: "EDAM:0000188 topic Sequence profiles and HMMs"
 
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  relations: "EDAM:0000351 operation Sequence database search
 
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                                     (by sequence using profile-based methods)"
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]
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section: input [
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           sequences, ii. set of sequences (unaligned or aligned, but
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           typically aligned sequences within a domain alignment file)). The
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           user has to specify which."
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    relations: "EDAM: Generic string array"                                
 
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    relations: "EDAM:0002527 data Parameter or primitive"
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  ]
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  dirlist: inseqspath [
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    default: "./"
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    extension: "daf"
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    knowntype: "domain alignment"
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    relations:  "EDAM: EMBASSY domain alignment file"                  
 
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    relations:  "EDAM:0001049 identifier Directory name"
 
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    relations:  "EDAM:0001384 data Sequence alignment (protein)"
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  ]
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  string: database [
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    information: "Name of BLAST-indexed database to search."
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    default: "swissprot"
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    knowntype: "blast protein dbname"
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    relations:  "EDAM: BLAST database name"                            
 
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    relations:  "EDAM:0001056 identifier Database name"
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  ]
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endsection: input
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           This option specifies the number of PSIBLAST iterations that are
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           performed in a search."
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    default: "1"
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    relations: "EDAM: Generic integer"                                     
 
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    relations: "EDAM:0001693 data Number of iterations"
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  ]
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  float: evalue [
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           in family. This option specifies the threshold E-value for a
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           PSIBLAST hit to be retained."
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    default: "0.001"
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    relations: "EDAM: Generic float"                                       
 
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    relations: "EDAM:0002146 data Threshold"
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  ]
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  integer: maxhits [
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           retained. It should normally be set high so that nothing is
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           discarded."
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    default: "1000"
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    relations: "EDAM: Generic integer"                                     
 
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    relations: "EDAM:0001694 data Number of output entities"
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  ]
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endsection: required
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    default: "./"
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    extension: "dhf"
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    knowntype: "domain hits"
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    relations:  "EDAM: EMBASSY domain hits report"                     
 
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    relations:  "EDAM:0001049 identifier Directory name"
 
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    relations: "EDAM:0000849 data Sequence record"
 
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    relations: "EDAM:0001219 format pure protein"
 
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    relations:  "EDAM:0000857 data Database hits (sequence)"
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  ]
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  outfile: logfile [
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           The log file contains messages about any errors arising while
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           SEQSEARCH ran."
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    knowntype: "domainatrix log"
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    relations:  "EDAM: Domainatrix log file"                           
 
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    relations:  "EDAM:0001678 data Tool log"
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  ]
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endsection: output