[2] | 1 | <tool id="lav_to_bed1" name="LAV to BED">
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| 2 | <description>Converts a LAV formatted file to BED format</description>
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| 3 | <command interpreter="python">lav_to_bed.py $lav_file $bed_file1 $bed_file2</command>
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| 4 | <inputs>
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| 5 | <param name="lav_file" type="data" format="lav" label="LAV File" optional="False"/>
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| 6 | </inputs>
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| 7 | <outputs>
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| 8 | <data name="bed_file1" format="bed"/>
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| 9 | <data name="bed_file2" format="bed"/>
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| 10 | </outputs>
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| 11 | <tests>
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| 12 | <test>
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| 13 | <param name="lav_file" value="2.lav" ftype="lav" />
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| 14 | <output name="bed_file2" file="lav_to_bed_out_1.bed" />
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| 15 | <output name="bed_file2" file="lav_to_bed_out_2.bed" />
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| 16 | </test>
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| 17 | </tests>
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| 18 | <help>
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| 19 |
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| 20 | **Syntax**
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| 21 |
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| 22 | This tool converts a LAV formatted file to the BED format.
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| 23 |
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| 24 | - **LAV format** LAV is an alignment format developed by Webb Miller's group at Penn State University. It is the primary output format for BLASTZ.
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| 25 |
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| 26 | - **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser.
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| 27 |
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| 28 | -----
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| 29 |
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| 30 | **Example**
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| 31 |
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| 32 | - Convert LAV format::
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| 33 |
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| 34 | #:lav
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| 35 | s {
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| 36 | "/galaxy/data/hg16/seq/chr19.nib" 1 63811651 0 1
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| 37 | "/galaxy/data/mm5/seq/chr11.nib" 1 121648857 0 1
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| 38 | }
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| 39 | h {
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| 40 | "> hg16.chr19"
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| 41 | "> mm5.chr11 (reverse complement)"
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| 42 | }
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| 43 | a {
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| 44 | s 3500
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| 45 | b 3001012 70568380
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| 46 | e 3001075 70568443
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| 47 | l 3001012 70568380 3001075 70568443 81
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| 48 | }
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| 49 | a {
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| 50 | s 3900
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| 51 | b 3008279 70573976
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| 52 | e 3008357 70574054
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| 53 | l 3008279 70573976 3008357 70574054 78
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| 54 | }
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| 55 | #:eof
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| 56 |
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| 57 | - To two BED formatted files::
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| 58 |
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| 59 | chr19 3001011 3001075 hg16_0 0 +
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| 60 | chr19 3008278 3008357 hg16_1 0 +
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| 61 |
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| 62 | **and**::
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| 63 |
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| 64 | chr11 70568379 70568443 mm5_0 0 +
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| 65 | chr11 70573975 70574054 mm5_1 0 +
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| 66 | </help>
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| 67 | <code file="lav_to_bed_code.py"/>
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| 68 | </tool>
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