comparison featureCounter.xml @ 0:56dab41a4c5f draft default tip

Imported from capsule None
author devteam
date Tue, 01 Apr 2014 09:12:47 -0400
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1 <tool id="featureCoverage1" name="Feature coverage" version="2.0.0">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.7.1">bx-python</requirement>
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
6 </requirements>
7 <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>
8 <inputs>
9 <param format="interval" name="input1" type="data" help="First dataset">
10 <label>What portion of</label>
11 </param>
12 <param format="interval" name="input2" type="data" help="Second dataset">
13 <label>is covered by</label>
14 </param>
15 </inputs>
16 <outputs>
17 <data format="interval" name="output" metadata_source="input1" />
18 </outputs>
19
20 <tests>
21 <test>
22 <param name="input1" value="1.bed" />
23 <param name="input2" value="2.bed" />
24 <output name="output" file="6_feature_coverage.bed" />
25 </test>
26 <test>
27 <param name="input1" value="chrY1.bed" />
28 <param name="input2" value="chrY2.bed" />
29 <output name="output" file="chrY_Coverage.bed" />
30 </test>
31 </tests>
32 <help>
33
34 .. class:: infomark
35
36 **What it does**
37
38 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.
39
40 -----
41
42 **Example**
43
44 - If **First dataset** consists of the following windows::
45
46 chrX 1 10001 seg 0 -
47 chrX 10001 20001 seg 0 -
48 chrX 20001 30001 seg 0 -
49 chrX 30001 40001 seg 0 -
50
51 - and **Second dataset** consists of the following exons::
52
53 chrX 5000 6000 seg2 0 -
54 chrX 5500 7000 seg2 0 -
55 chrX 9000 22000 seg2 0 -
56 chrX 24000 34000 seg2 0 -
57 chrX 36000 38000 seg2 0 -
58
59 - the **Result** is the coverage of exons of the second dataset in each of the windows contained in first dataset::
60
61 chrX 1 10001 seg 0 - 3001 0.3001 2 1
62 chrX 10001 20001 seg 0 - 10000 1.0 1 0
63 chrX 20001 30001 seg 0 - 8000 0.8 0 2
64 chrX 30001 40001 seg 0 - 5999 0.5999 1 1
65
66 - To clarify, the following line of output ( added columns are indexed by a, b and c )::
67
68 a b c d
69 chrX 1 10001 seg 0 - 3001 0.3001 2 1
70
71 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).
72
73 * 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)
74 * b: fraction of window size covered by features in (c) and (d) - features overlapping with each other will be merged to calculate (b)
75 * c: number of features in the 2nd dataset that fall **completely** within this window
76 * d: number of features in the 2nd dataset that **partially** overlap this window
77
78 </help>
79 </tool>