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72 lines
2.6 KiB
XML
72 lines
2.6 KiB
XML
<tool id="featureCoverage" name="Feature coverage">
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<description></description>
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<command interpreter="python2.4">featureCounter.py $input1 $input2 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -2 $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol</command>
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<inputs>
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<param format="interval" name="input1" type="data" help="First query">
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<label>What portion of</label>
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</param>
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<param format="interval" name="input2" type="data" help="Second query">
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<label>is covered by</label>
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</param>
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</inputs>
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<outputs>
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<data format="interval" name="output" metadata_source="input1" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="1.bed" />
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<param name="input2" value="2.bed" />
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<output name="output" file="6_feature_coverage.bed" />
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</test>
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</tests>
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<help>
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.. class:: infomark
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**What it does**
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This tool finds the coverage of intervals in the first query on intervals in the second query. The count and coverage are added as 4 new columns, as explained in the example below.
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-----
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**Example**
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- if **First query** consists of following windows::
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chrX 1 10001 seg 0 -
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chrX 10001 20001 seg 0 -
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chrX 20001 30001 seg 0 -
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chrX 30001 40001 seg 0 -
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- and **Second query** consits of following exons::
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chrX 5000 6000 seg2 0 -
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chrX 5500 7000 seg2 0 -
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chrX 9000 22000 seg2 0 -
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chrX 24000 34000 seg2 0 -
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chrX 36000 38000 seg2 0 -
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- the **Result** is the coverage of exons of second query in each of the windows contained in first query::
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chrX 1 10001 seg 0 - 2 20.00 1 10.00
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chrX 10001 20001 seg 0 - 1 100.00 0 0.00
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chrX 20001 30001 seg 0 - 0 0.00 2 80.00
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chrX 30001 40001 seg 0 - 1 20.00 1 39.99
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- For example, the following line of output (New columns added are indexed by a-d below)::
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chrX 1 10001 seg 0 - 2 20.00 1 10.00
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a b c d
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implies that 2 exons(a) fall in this window(chrX:1-10001) completely covering 20% of the window size(b) and 1 exon(c) partially overlaps with this window, covering 10% of the window size(d).
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a : Number of features in the 2nd query that fall COMPLETELY within this window
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b : % of window size covered by features in 'a' (All overlapping features in 'a' will be merged to calculate 'b')
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c : Number of features in the 2nd query that partiallyoverlap with this window
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d : % of window size covered by features in 'c' (All overlapping features in 'c' will be merged to calculate 'd')
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</help>
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</tool>
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