Mercurial > repos > xuebing > sharplabtool
comparison tools/regVariation/featureCounter.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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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 | |
| 34 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. | |
| 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> |