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1 <tool id="blat2wig" name="Coverage of the Reads" version="1.0.0">
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2 <description>in wiggle format</description>
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3 <command interpreter="python">blat_mapping.py $input1 $output1</command>
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4 <inputs>
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5 <param name="input1" type="data" format="tabular" label="Alignment result"/>
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6 </inputs>
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7 <outputs>
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8 <data name="output1" format="wig"/>
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9 </outputs>
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10 <tests>
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11 <test>
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12 <param name="input1" value="blat_mapping_test1.txt" ftype="tabular" />
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13 <output name="output1" file="blat_mapping_test1.out" />
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14 </test>
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15 </tests>
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16 <help>
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17
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18 .. class:: warningmark
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19
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20 To generate acceptable files, please use alignment program **BLAT** with option **-out=pslx**.
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21
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22 .. class:: warningmark
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23
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24 Please edit the database information by click on the pencil icon next to your dataset. Select the corresponding genome build.
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25
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26 -----
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27
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28 **What it does**
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29
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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.
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31
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32 -----
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33
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34 **Example**
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35
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36 Showing reads coverage on human chromosome 22 (partial result) in UCSC Genome Browser Custom Track:
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37
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38 .. image:: blat_mapping_example.png
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39 :width: 600
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40
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41 </help>
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42 </tool>
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