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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/revcompl.uwl
 
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#!UGENE_WORKFLOW
 
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#Convert input sequence into its reverse, complement or reverse-complement counterpart and write result sequence to file
 
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workflow revcompl{
 
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    reverse-complement {
 
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        type:reverse-complement;
 
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        name:"Reverse Complement";
 
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        op-type:reverse-complement;
 
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    }
 
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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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    write-sequence {
 
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        type:write-sequence;
 
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        name:"Write sequence";
 
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        accumulate:true;
 
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        document-format:fasta;
 
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        write-mode:2;
 
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    }
 
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    read-sequence.sequence->reverse-complement.in-sequence.sequence
 
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    read-sequence.annotations->write-sequence.in-sequence.annotations
 
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    reverse-complement.sequence->write-sequence.in-sequence.sequence
 
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    .iteration "Default iteration"{
 
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        id:4;
 
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        reverse-complement {
 
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            op-type:reverse-complement;
 
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        }
 
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    }
 
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    .meta {
 
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        aliases {
 
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            reverse-complement.op-type:type;
 
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            read-sequence.url-in:in;
 
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            write-sequence.document-format:format;
 
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            write-sequence.url-out:out;
 
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        }
 
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        help {
 
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            type:"Type of operation. Reverse-complement by default, 'norev' for complement only and 'nocompl' for reverse only";
 
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            in:"Input file";
 
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            format:"Output file format";
 
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            out:"Output file";
 
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        }
 
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        visual {
 
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            reverse-complement {
 
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                description:"<!DOCTYPE HTML PUBLIC '-//W3C//DTD HTML 4.0//EN' 'http://www.w3.org/TR/REC-html40/strict.dtd'> <html><head><meta name='qrichtext' content='1' /><style type='text/css'> p, li { white-space: pre-wrap; } </style></head><body style=' font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;'> <p align='center' style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'><span style=' font-weight:600;'>Reverse Complement</span></p> <hr /> <p style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'>Converts a sequence from from <span style=' text-decoration: underline;'>Read sequence</span> into its reverse-complement counterpart</p></body></html>";
 
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                tooltip:"Converts input sequence into its reverse, complement or reverse-complement counterpart";
 
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                pos:"-525 -585";
 
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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-sequence.angle:360;
 
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            }
 
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            read-sequence {
 
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                description:"<!DOCTYPE HTML PUBLIC '-//W3C//DTD HTML 4.0//EN' 'http://www.w3.org/TR/REC-html40/strict.dtd'> <html><head><meta name='qrichtext' content='1' /><style type='text/css'> p, li { white-space: pre-wrap; } </style></head><body style=' font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;'> <p align='center' style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'><span style=' font-weight:600;'>Read sequence</span></p> <hr /> <p style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'>Reads sequence(s) from <span style=' text-decoration: underline; color:#ff0000;'>unset</span>.</p></body></html>";
 
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                tooltip:"Reads sequences and annotations if any from local or remote files.";
 
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                pos:"-705 -585";
 
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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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            read-sequence.out-sequence->reverse-complement.in-sequence {
 
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                text-pos:"-27.5 -24";
 
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            }
 
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            write-sequence {
 
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                description:"<!DOCTYPE HTML PUBLIC '-//W3C//DTD HTML 4.0//EN' 'http://www.w3.org/TR/REC-html40/strict.dtd'> <html><head><meta name='qrichtext' content='1' /><style type='text/css'> p, li { white-space: pre-wrap; } </style></head><body style=' font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;'> <p align='center' style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'><span style=' font-weight:600;'>Write sequence</span></p> <hr /> <p style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'>Save all sequences from <span style=' text-decoration: underline;'>Reverse Complement</span> to <span style=' text-decoration: underline; color:#ff0000;'>unset</span>.</p></body></html>";
 
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                tooltip:"Writes all supplied sequences to file(s) in selected format.";
 
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                pos:"-285 -585";
 
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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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            reverse-complement.out-sequence->write-sequence.in-sequence {
 
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                text-pos:"-45 -37";
 
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            }
 
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        }
 
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    }
 
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}
 
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