comparison tabix.xml @ 3:5ff4702264f7 draft

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author nilesh
date Wed, 10 Jul 2013 15:07:14 -0400
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1 <tool id="tabix" name="tabix" version="0.0.1">
2 <description>Generic indexer for TAB-delimited genome position files.</description>
3 <requirements>
4 <requirement type="package" version= "0.2.6">tabix</requirement>
5 </requirements>
6 <command>
7 tabix
8 #if str($position) == "no"
9 -0
10 #end if
11
12 #if str($options.extension) == "tabular"
13 #if str($options.columnseq) != ""
14 -s $options.columnseq
15 #end if
16
17 #if str($options.columnstart) != ""
18 -b $options.columnstart
19 #end if
20
21 #if str($options.columnend) != ""
22 -e $options.columnend
23 #end if
24
25 #if str($options.skiplines) != ""
26 -S $options.skiplines
27 #end if
28
29 #if str($options.skipchar) != ""
30 -c $options.skipchar
31 #end if
32 #else
33 -p
34 #end if
35
36 $input $region
37
38 </command>
39 <inputs>
40 <param name="input" type="data" label="Input file" format="gff,bed,sam,vcf,tabular">
41 </param>
42 <param name="region" type="text" optional="true" label="Regions (seperate with spaces)"> </param>
43 <conditional name="optional">
44 <param name= "extension" type="select" value= "tabular" label= "Input Extension">
45 <option value="tabular">tabular</option>
46 <option value="gff">gff</option>
47 <option value="bed">bed</option>
48 <option value="sam">sam</option>
49 <option value="vcf">vcf</option>
50 </param>
51 <when value="tabular">
52 <param name="columnseq" type="integer" optional= "true" label="Column of sequence name" />
53 <param name="columnstart" type="integer" optional= "true" label="Column of start chromosomal position" />
54 <param name="columnend" type="integer" optional= "true" label="Column of end chromosomal position" />
55 <param name="skiplines" type="integer" optional= "true" label="Skip first INT lines" />
56 <param name="skipchar" type="text" optional= "true" label="Skip lines started with CHAR" />
57 <param name="position" type= "select" value= "yes" label="1-based? (if not, 0-based)">
58 <option value= "yes">yes</option>
59 <option value= "no">no</option>
60 </param>
61 </when>
62 </conditional>
63 </inputs>
64
65 <outputs>
66 <data format="tabular" name="output" />
67 </outputs>
68
69 <help>
70 **What it does:**
71
72 Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.
73
74 **Citation:**
75
76 Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching.
77
78 http://samtools.sourceforge.net/tabix.shtml
79
80 **Example:**
81
82 (grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
83
84 tabix -p gff sorted.gff.gz;
85
86 tabix sorted.gff.gz chr1:10,000,000-20,000,000;
87
88 </help>
89 </tool>