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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/workflow_samples/DNA assembly/gen-al-read-index.uwl
 
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#!UGENE_WORKFLOW
 
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#Aligns short reads to reference genome using a pre-built genome aligner index. The output alignment is saved to SAM format. To execute the schema do the following:1) Select "Read sequence" task and specify source file(s) at "URL" field in the Property Editor.2) Select "Genome aligner index reader" task and specify URL to the pre-built index.3) Specify genome aligner options in the properties of "UGENE genome aligner" task.4) Launch the schema with pressing Ctrl+R shrotcut.After running the schema, the alignment file will appear in the same folder as the source file. Pre-built indxeses can be built by UGENE genome aligner index builder.
 
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#
 
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#
 
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workflow "Align to reference genome with UGENE genome aligner"{
 
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    gen-al-read-index {
 
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        type:gen-al-read-index;
 
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        name:"Genome aligner index reader";
 
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    }
 
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    read-sequence {
 
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        type:read-sequence;
 
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        name:"Short-reads reader";
 
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        merge-gap:10;
 
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        mode:0;
 
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    }
 
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    genome-aligner {
 
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        type:genome-aligner;
 
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        name:"UGENE genome aligner";
 
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        absolute-mismatches:0;
 
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        best:false;
 
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        gpu:false;
 
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        if-absolute-mismatches-value:false;
 
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        percentage-mismatches:0;
 
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        quality-threshold:0;
 
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        reverse:true;
 
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    }
 
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    write-msa {
 
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        type:write-msa;
 
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        name:"SAM writer";
 
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        document-format:clustal;
 
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        write-mode:2;
 
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    }
 
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    gen-al-read-index.gen-al-index-slot->genome-aligner.in-gen-al-index.gen-al-index-slot
 
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    read-sequence.sequence->genome-aligner.in-sequence.sequence
 
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    genome-aligner.msa->write-msa.in-msa.msa
 
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    .iteration "Default iteration"{
 
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        id:6;
 
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        write-msa {
 
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            document-format:sam;
 
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        }
 
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    }
 
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    .meta {
 
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        visual {
 
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            gen-al-read-index {
 
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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;'>Genome aligner index reader</span></p> <hr /> <p style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'>Read genome aligner index from and send it url to output.</p></body></html>";
 
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                tooltip:"Read a set of several files with extensions .idx, .ref, .X.sarr. These files together constitute the index: they are all that is needed to align reads to that reference.";
 
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                pos:"-780 -555";
 
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                style:ext;
 
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                bg-color-ext:"0 128 128 64";
 
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                out-gen-al-index.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;'>Short-reads reader</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:"-765 -390";
 
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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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            genome-aligner {
 
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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;'>UGENE genome aligner</span></p> <hr /> <p style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'>Align short reads to the reference genome and send it to output.</p></body></html>";
 
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                tooltip:"Unique UGENE algorithm for aligning short reads to reference genome";
 
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                pos:"-540 -465";
 
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                style:ext;
 
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                bg-color-ext:"0 128 128 64";
 
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                in-gen-al-index.angle:150;
 
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                in-sequence.angle:210;
 
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                out-msa.angle:360;
 
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            }
 
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            write-msa {
 
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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;'>SAM writer</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 MSAs from <span style=' text-decoration: underline;'>UGENE genome aligner</span> to <span style=' text-decoration: underline; color:#ff0000;'>unset</span>.</p></body></html>";
 
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                tooltip:"Writes all supplied alignments to file(s) in selected format";
 
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                pos:"-300 -465";
 
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                style:ext;
 
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                bg-color-ext:"0 128 128 64";
 
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                in-msa.angle:180;
 
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            }
 
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            gen-al-read-index.out-gen-al-index->genome-aligner.in-gen-al-index {
 
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                text-pos:"-45 -37";
 
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            }
 
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            read-sequence.out-sequence->genome-aligner.in-sequence {
 
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                text-pos:"-27.5 -24";
 
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            }
 
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            genome-aligner.out-msa->write-msa.in-msa {
 
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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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