PageRenderTime 18ms CodeModel.GetById 11ms app.highlight 3ms RepoModel.GetById 1ms app.codeStats 0ms

/tools/filters/lav_to_bed.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 68 lines | 56 code | 12 blank | 0 comment | 0 complexity | e2ddd11f6f2e3573084de941452b70e6 MD5 | raw file
 1<tool id="lav_to_bed1" name="LAV to BED">
 2  <description>Converts a LAV formatted file to BED format</description>
 3  <command interpreter="python">lav_to_bed.py $lav_file $bed_file1 $bed_file2</command>
 4  <inputs>
 5    <param name="lav_file" type="data" format="lav" label="LAV File" optional="False"/>
 6  </inputs>
 7  <outputs>
 8    <data name="bed_file1" format="bed"/>
 9    <data name="bed_file2" format="bed"/>
10  </outputs>
11  <tests>
12    <test>
13      <param name="lav_file" value="2.lav" ftype="lav" />
14      <output name="bed_file2" file="lav_to_bed_out_1.bed" />
15      <output name="bed_file2" file="lav_to_bed_out_2.bed" />
16    </test>
17  </tests>
18  <help>
19
20**Syntax**
21
22This tool converts a LAV formatted file to the BED format.
23
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.
25
26- **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser.
27
28-----
29
30**Example**
31
32- Convert LAV format::
33
34    #:lav
35    s {
36      &quot;/galaxy/data/hg16/seq/chr19.nib&quot; 1 63811651 0 1
37      &quot;/galaxy/data/mm5/seq/chr11.nib&quot; 1 121648857 0 1
38    }
39    h {
40      &quot;> hg16.chr19&quot;
41      &quot;> mm5.chr11 (reverse complement)&quot;
42    }
43    a {
44      s 3500
45      b 3001012 70568380
46      e 3001075 70568443
47      l 3001012 70568380 3001075 70568443 81
48    }
49    a {
50      s 3900
51      b 3008279 70573976
52      e 3008357 70574054
53      l 3008279 70573976 3008357 70574054 78
54    }
55    #:eof
56
57- To two BED formatted files::
58
59    chr19	3001011	3001075	hg16_0	0	+
60    chr19	3008278	3008357	hg16_1	0	+
61    
62 **and**::
63    
64    chr11	70568379	70568443	mm5_0	0	+
65    chr11	70573975	70574054	mm5_1	0	+
66  </help>
67  <code file="lav_to_bed_code.py"/>
68</tool>