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70 lines
2.4 KiB
XML
70 lines
2.4 KiB
XML
<tool id="featureCoverage1" name="Feature coverage" version="1.0.0">
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<description></description>
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<command interpreter="python">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 3 new columns in the resulting dataset.
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-----
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**Example**
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- If **First query** consists of the 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** consists of the 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 the second query in each of the windows contained in first query::
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chrX 1 10001 seg 0 - 2 1 30.01
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chrX 10001 20001 seg 0 - 1 0 100.00
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chrX 20001 30001 seg 0 - 0 2 80.00
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chrX 30001 40001 seg 0 - 1 1 59.99
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- To clarify, the following line of output ( added columns are indexed by a, b and c )::
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a b c
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chrX 1 10001 seg 0 - 2 1 30.01
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implies that 2 exons (a) fall into this window ( chrX:1-10001 ), 1 exon (b) partially overlaps this window, and these 3 exons cover 30.01% of the window size (c).
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* a: number of features in the 2nd query that fall **completely** within this window
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* b: number of features in the 2nd query that partially overlap this window
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* c: % of window size covered by features in (a) and (b) - features overlapping with each other will be merged to calculate (c)
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</help>
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</tool>
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