root/galaxy-central/tools/metag_tools/blat_mapping.xml

リビジョン 2, 1.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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/images/blat_mapping_example.png
39        :width: 600
40       
41  </help>
42</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。