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76 lines
2.9 KiB
XML
76 lines
2.9 KiB
XML
<tool id="featureCoverage1" name="Feature coverage" version="2.0.0">
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<description></description>
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<command interpreter="python">featureCounter.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}</command>
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<inputs>
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<param format="interval" name="input1" type="data" help="First dataset">
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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 dataset">
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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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<test>
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<param name="input1" value="chrY1.bed" />
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<param name="input2" value="chrY2.bed" />
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<output name="output" file="chrY_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 dataset on intervals in the second dataset. The coverage and count are appended as 4 new columns in the resulting dataset.
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-----
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**Example**
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- If **First dataset** 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 dataset** 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 dataset in each of the windows contained in first dataset::
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chrX 1 10001 seg 0 - 3001 0.3001 2 1
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chrX 10001 20001 seg 0 - 10000 1.0 1 0
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chrX 20001 30001 seg 0 - 8000 0.8 0 2
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chrX 30001 40001 seg 0 - 5999 0.5999 1 1
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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 d
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chrX 1 10001 seg 0 - 3001 0.3001 2 1
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implies that 2 exons (c) fall fully in this window (chrX:1-10001), 1 exon (d) partially overlaps this window, and these 3 exons cover 30.01% (c) of the window size, spanning 3001 nucleotides (a).
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* a: number of nucleotides in this window covered by the features in (c) and (d) - features overlapping with each other will be merged to calculate (a)
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* b: fraction of window size covered by features in (c) and (d) - features overlapping with each other will be merged to calculate (b)
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* c: number of features in the 2nd dataset that fall **completely** within this window
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* d: number of features in the 2nd dataset that **partially** overlap this window
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</help>
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</tool>
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