diff tools/metag_tools/blat_mapping.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/metag_tools/blat_mapping.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,42 @@
+<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/images/blat_mapping_example.png
+ 	:width: 600
+ 	
+  </help>
+</tool>