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1 <tool id="featureCoverage1" name="Feature coverage" version="2.0.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
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6 </requirements>
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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>
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8 <inputs>
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9 <param format="interval" name="input1" type="data" help="First dataset">
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10 <label>What portion of</label>
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11 </param>
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12 <param format="interval" name="input2" type="data" help="Second dataset">
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13 <label>is covered by</label>
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14 </param>
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15 </inputs>
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16 <outputs>
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17 <data format="interval" name="output" metadata_source="input1" />
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18 </outputs>
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19
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20 <tests>
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21 <test>
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22 <param name="input1" value="1.bed" />
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23 <param name="input2" value="2.bed" />
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24 <output name="output" file="6_feature_coverage.bed" />
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25 </test>
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26 <test>
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27 <param name="input1" value="chrY1.bed" />
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28 <param name="input2" value="chrY2.bed" />
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29 <output name="output" file="chrY_Coverage.bed" />
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30 </test>
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31 </tests>
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32 <help>
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33
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34 .. class:: infomark
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35
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36 **What it does**
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37
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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.
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39
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40 -----
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41
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42 **Example**
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43
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44 - If **First dataset** consists of the following windows::
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45
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46 chrX 1 10001 seg 0 -
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47 chrX 10001 20001 seg 0 -
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48 chrX 20001 30001 seg 0 -
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49 chrX 30001 40001 seg 0 -
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50
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51 - and **Second dataset** consists of the following exons::
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52
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53 chrX 5000 6000 seg2 0 -
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54 chrX 5500 7000 seg2 0 -
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55 chrX 9000 22000 seg2 0 -
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56 chrX 24000 34000 seg2 0 -
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57 chrX 36000 38000 seg2 0 -
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58
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59 - the **Result** is the coverage of exons of the second dataset in each of the windows contained in first dataset::
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60
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61 chrX 1 10001 seg 0 - 3001 0.3001 2 1
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62 chrX 10001 20001 seg 0 - 10000 1.0 1 0
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63 chrX 20001 30001 seg 0 - 8000 0.8 0 2
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64 chrX 30001 40001 seg 0 - 5999 0.5999 1 1
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65
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66 - To clarify, the following line of output ( added columns are indexed by a, b and c )::
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67
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68 a b c d
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69 chrX 1 10001 seg 0 - 3001 0.3001 2 1
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70
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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).
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72
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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)
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74 * 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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75 * c: number of features in the 2nd dataset that fall **completely** within this window
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76 * d: number of features in the 2nd dataset that **partially** overlap this window
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77
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78 </help>
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79 </tool>
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