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  • Committer: Package Import Robot
  • Author(s): Steffen Moeller
  • Date: 2011-11-02 13:29:07 UTC
  • mfrom: (1.2.1) (3.1.11 natty)
  • Revision ID: package-import@ubuntu.com-20111102132907-o34gwnt0uj5g6hen
Tags: 1.9.8+repack-1
* First release to Debian
  - added README.Debian
  - increased policy version to 3.9.2
  - added URLs for version control system
* Added debug package.

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data/cmdline/remote-request.uwl
 
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#!UGENE_WORKFLOW
 
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#Finds annotations for DNA sequence in remote database: NCBI BLSAT or CDD. Result annotations store to file in genbank format. Source data can be of any format containing sequences or alignments
 
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workflow remote-request{
 
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    read-sequence {
 
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        type:read-sequence;
 
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        name:"Read sequence";
 
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        merge-gap:10;
 
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        mode:0;
 
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    }
 
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    blast-ncbi {
 
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        type:blast-ncbi;
 
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        name:"Request to remote database";
 
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        db:ncbi-blastn;
 
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        e-val:10;
 
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        max-hits:10;
 
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        short-sequence:false;
 
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    }
 
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    write-genbank {
 
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        type:write-genbank;
 
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        name:"Write Genbank";
 
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        accumulate:true;
 
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        write-mode:2;
 
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    }
 
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    read-sequence.sequence->blast-ncbi.in-sequence.sequence
 
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    blast-ncbi.annotations->write-genbank.in-sequence.annotations
 
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    read-sequence.annotations->write-genbank.in-sequence.annotations
 
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    read-sequence.sequence->write-genbank.in-sequence.sequence
 
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    .meta {
 
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        aliases {
 
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            read-sequence.url-in:in;
 
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            blast-ncbi.blast-output:blast-output;
 
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            blast-ncbi.db:db;
 
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            blast-ncbi.e-val:eval;
 
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            blast-ncbi.max-hits:hits;
 
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            blast-ncbi.result-name:name;
 
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            blast-ncbi.short-sequence:short;
 
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            write-genbank.url-out:out;
 
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        }
 
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        help {
 
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            in:"Input sequence";
 
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            blast-output:"Location of BLAST output file";
 
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            db:"The database to search through";
 
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            eval:"The statistical significance threshold of reporting matches against the database sequences";
 
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            hits:"Maximum number of hits";
 
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            name:"Name of the result annotations";
 
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            short:"Optimize search for short sequences";
 
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            out:"Output file with annotations";
 
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        }
 
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        visual {
 
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            read-sequence {
 
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                tooltip:"Reads sequences and annotations if any from local or remote files.";
 
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                pos:"-780 -630";
 
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                style:ext;
 
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                bg-color-ext:"0 128 128 64";
 
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                out-sequence.angle:360;
 
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            }
 
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            blast-ncbi {
 
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                tooltip:"Finds annotations for DNA sequence in remote database";
 
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                pos:"-600 -630";
 
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                style:ext;
 
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                bg-color-ext:"0 128 128 64";
 
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                in-sequence.angle:180;
 
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                out-annotations.angle:360;
 
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            }
 
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            write-genbank {
 
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                tooltip:"Writes all supplied sequences and related annotations to file(s) in Genbank format.";
 
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                pos:"-360 -630";
 
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                style:ext;
 
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                bg-color-ext:"0 128 128 64";
 
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                in-sequence.angle:180;
 
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            }
 
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            read-sequence.out-sequence->blast-ncbi.in-sequence {
 
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                text-pos:"-27.5 -24";
 
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            }
 
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            blast-ncbi.out-annotations->write-genbank.in-sequence {
 
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                text-pos:"-33 -24";
 
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            }
 
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        }
 
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    }
 
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}
 
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