/tools/metag_tools/blat_mapping.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 42 lines · 30 code · 12 blank · 0 comment · 0 complexity · 76e3a3f4d57a2b353f1f0a9de4597e8a MD5 · raw file
- <tool id="blat2wig" name="Coverage of the Reads">
- <description>in wiggle format</description>
- <command interpreter="python">blat_mapping.py $input1 $output1</command>
- <inputs>
- <param name="input1" type="data" format="tabular" label="Alignment result"/>
- </inputs>
- <outputs>
- <data name="output1" format="wig"/>
- </outputs>
- <tests>
- <test>
- <param name="input1" value="blat_mapping_test1.txt" ftype="tabular" />
- <output name="output1" file="blat_mapping_test1.out" />
- </test>
- </tests>
- <help>
- .. class:: warningmark
- To generate acceptable files, please use alignment program **BLAT** with option **-out=pslx**.
- .. class:: warningmark
- Please edit the database information by click on the pencil icon next to your dataset. Select the corresponding genome build.
- -----
-
- **What it does**
-
- 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.
- -----
- **Example**
- Showing reads coverage on human chromosome 22 (partial result) in UCSC Genome Browser Custom Track:
-
- .. image:: ${static_path}/images/blat_mapping_example.png
- :width: 600
-
- </help>
- </tool>