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1 <tool id="bedtools_genomecoveragebed_histogram" name="Create a histogram of genome coverage" version="0.1.0">
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2 <description></description>
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11
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3
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4 <requirements>
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5 <requirement type="binary">genomeCoverageBed</requirement>
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6 </requirements>
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7
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8 <command>genomeCoverageBed
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9 #if $input.ext == "bam"
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10 -ibam '$input'
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11 #else
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12 -i '$input'
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13 -g ${chromInfo}
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14 #end if
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15 #if str($max):
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16 -max $max
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17 #end if
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18 > '$output'
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19 </command>
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20
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21 <inputs>
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22 <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed"></param>
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23 <param name="max" type="text" optional="true" label="Max depth" help="Combine all positions with a depth >= max into a single bin in the histogram."/>
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24 </inputs>
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25
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26 <outputs>
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27 <data format="tabular" name="output" metadata_source="input" label="${input.name} (Genome Coverage Histogram)" />
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28 </outputs>
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29
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30 <help>
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31 **What it does**
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32
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33 This tool calculates a histogram of genome coverage depth based on mapped reads in BAM format or intervals in BED format.
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34
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35
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36 ------
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37
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38 .. class:: warningmark
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39
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40 This tool requires that `bedtools`__ has been installed on your system.
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41
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42 .. class:: infomark
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43
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44 The output file will contain five columns:
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45
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46 * 1. Chromosome name (or 'genome' for whole-genome coverage)
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47 * 2. Coverage depth
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48 * 3. The number of bases on chromosome (or genome) with depth equal to column 2.
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49 * 4. The size of chromosome (or entire genome) in base pairs
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50 * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.
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51
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52 **Example Output**::
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53
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54 chr2L 0 1379895 23011544 0.0599653
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55 chr2L 1 837250 23011544 0.0363839
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56 chr2L 2 904442 23011544 0.0393038
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57 chr2L 3 913723 23011544 0.0397072
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58 chr2L 4 952166 23011544 0.0413778
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59 chr2L 5 967763 23011544 0.0420555
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60 chr2L 6 986331 23011544 0.0428624
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61 chr2L 7 998244 23011544 0.0433801
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62 chr2L 8 995791 23011544 0.0432735
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63 chr2L 9 996398 23011544 0.0432999
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64
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65
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66
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67
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68 ------
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69
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70 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
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71
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72 .. __: http://code.google.com/p/bedtools/
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73 .. __: http://code.google.com/p/bedtools/
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74 .. __: http://cphg.virginia.edu/quinlan/
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75 .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
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76
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77
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78
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79 </help>
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80 </tool>
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