/tools/metag_tools/blat_mapping.xml

 1<tool id="blat2wig" name="Coverage of the Reads">
 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:: ${static_path}/images/blat_mapping_example.png
39 	:width: 600
40 	
41  </help>
42</tool>