Mercurial > repos > xuebing > sharplabtool
comparison mytools/bowtie2bed.xml @ 7:f0dc65e7f6c0
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author | xuebing |
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date | Fri, 09 Mar 2012 19:59:07 -0500 |
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6:094f377db4e5 | 7:f0dc65e7f6c0 |
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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> |