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comparison mytools/bowtie2bed.xml @ 0:39217fa39ff2

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author xuebing
date Tue, 13 Mar 2012 23:34:52 -0400
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1 <tool id="bowtie2bed" name="bowtie-to-bed">
2 <description> converter and read extender</description>
3 <command interpreter="perl">bowtie2bed.pl $input $out_file1 $extendLength </command>
4 <inputs>
5 <param name="input" format="txt" type="data" label="Bowtie map result file"/>
6 <param name="extendLength" size="10" type="integer" value="200" label="Extend 3 primer (bp)"/>
7 </inputs>
8 <outputs>
9 <data format="bed" name="out_file1" />
10 </outputs>
11 <tests>
12 <test>
13 <param name="input" value="test.map" ftype="TXT"/>
14 <param name="extendLength" value="200"/>
15 <output name="out_file1" file="testmap.bed"/>
16 </test>
17 </tests>
18 <help>
19
20
21 **What it does**
22
23 This tool converts bowtie output map format file to bed format, with the option to extend the 3 primer end.
24
25 - Sequence and quality information is lost after conversion
26 - The output contains a track name at the first row
27
28 -----
29
30 **Example**
31
32 Converting the following bowtie mapped reads::
33
34 SRR073078.2 HWUSI-EAS465_8_1_1_524 length=36 - chr2 112499209 AGTGTGACTGCATCTCTTCCTTCGTGGGGCTNCAGT ...
35 SRR073078.3 HWUSI-EAS465_8_1_1_1054 length=36 + chr17 75877120 CCACNCCTCCTTTCAAAACACACTGCCAGGTGCGTC ...
36
37 will result in::
38
39 track name=/home/xuebing/Research/galaxy/galaxy-dist/database/files/000/dataset_5.dat itemRgb=On
40 chr2 112499109 112499245 SRR073078.2-HWUSI-EAS465_8_1_1_524-length=36 1 - 112499209 112499245 0,255,0
41 chr17 75877120 75877256 SRR073078.3-HWUSI-EAS465_8_1_1_1054-length=36 1 + 75877120 75877156 255,0,0
42
43 </help>
44 </tool>