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Imported from capsule None
author devteam
date Mon, 19 May 2014 12:33:35 -0400
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1 <tool id="blat2wig" name="Coverage of the Reads" version="1.0.0">
2 <description>in wiggle format</description>
3 <command interpreter="python">blat_mapping.py $input1 $output1</command>
4 <inputs>
5 <param name="input1" type="data" format="tabular" label="Alignment result"/>
6 </inputs>
7 <outputs>
8 <data name="output1" format="wig"/>
9 </outputs>
10 <tests>
11 <test>
12 <param name="input1" value="blat_mapping_test1.txt" ftype="tabular" />
13 <output name="output1" file="blat_mapping_test1.out" />
14 </test>
15 </tests>
16 <help>
17
18 .. class:: warningmark
19
20 To generate acceptable files, please use alignment program **BLAT** with option **-out=pslx**.
21
22 .. class:: warningmark
23
24 Please edit the database information by click on the pencil icon next to your dataset. Select the corresponding genome build.
25
26 -----
27
28 **What it does**
29
30 This tool takes **BLAT pslx** output and returns a wig-like file showing the number of reads (coverage) mapped at each chromosome location. Use **Graph/Display Data --> Build custom track** tool to show the coverage mapping in UCSC Genome Browser.
31
32 -----
33
34 **Example**
35
36 Showing reads coverage on human chromosome 22 (partial result) in UCSC Genome Browser Custom Track:
37
38 .. image:: blat_mapping_example.png
39 :width: 600
40
41 </help>
42 </tool>