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/tools/regVariation/featureCounter.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="featureCoverage1" name="Feature coverage" version="2.0.0">
 2  <description></description>
 3  <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>
 4  <inputs>
 5    <param format="interval" name="input1" type="data" help="First dataset">
 6      <label>What portion of</label>
 7    </param>
 8    <param format="interval" name="input2" type="data" help="Second dataset">
 9      <label>is covered by</label>
10    </param>
11   </inputs>
12  <outputs>
13    <data format="interval" name="output" metadata_source="input1" />
14  </outputs>
15  
16  <tests>
17    <test>
18      <param name="input1" value="1.bed" />
19      <param name="input2" value="2.bed" />
20      <output name="output" file="6_feature_coverage.bed" />
21    </test>
22    <test>
23      <param name="input1" value="chrY1.bed" />
24      <param name="input2" value="chrY2.bed" />
25      <output name="output" file="chrY_Coverage.bed" />
26    </test>
27  </tests>
28  <help>
29
30.. class:: infomark
31
32**What it does**
33
34This 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.
35
36-----
37
38**Example**
39
40- If **First dataset** consists of the following windows::
41
42    chrX 1     10001 seg 0 -
43    chrX 10001 20001 seg 0 -
44    chrX 20001 30001 seg 0 -
45    chrX 30001 40001 seg 0 -
46      
47- and **Second dataset** consists of the following exons::
48
49    chrX 5000  6000  seg2 0 -
50    chrX 5500  7000  seg2 0 -
51    chrX 9000  22000 seg2 0 -
52    chrX 24000 34000 seg2 0 -
53    chrX 36000 38000 seg2 0 -
54      
55- the **Result** is the coverage of exons of the second dataset in each of the windows contained in first dataset::
56
57    chrX 1     10001 seg 0 - 3001  0.3001 2 1
58    chrX 10001 20001 seg 0 - 10000 1.0    1 0
59    chrX 20001 30001 seg 0 - 8000  0.8    0 2
60    chrX 30001 40001 seg 0 - 5999  0.5999 1 1
61	  
62- To clarify, the following line of output ( added columns are indexed by a, b and c )::
63
64                         a    b      c d
65    chrX 1 10001 seg 0 - 3001 0.3001 2 1
66                                  
67  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).
68
69  * 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)
70  * b: fraction of window size covered by features in (c) and (d) - features overlapping with each other will be merged to calculate (b)
71  * c: number of features in the 2nd dataset that fall **completely** within this window
72  * d: number of features in the 2nd dataset that **partially** overlap this window
73  	 
74</help>
75</tool>