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annotate coverageBed.xml @ 24:679fbed9d08f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9555dac6cbff70048b682a6514c7fbb2b7fbb975
author iuc
date Mon, 05 Sep 2016 15:27:44 -0400
parents ac8b17b66663
children 6c6963cf9136
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1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
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2 <description>
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3 of features in file B on the features in file A (bedtools coverage)
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <command>
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11 <![CDATA[
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12 #set inputBs = "' '".join([str($file) for $file in $inputB])
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14 bedtools coverage
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15 $d
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16 $hist
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17 $split
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18 $strandedness
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19 -a '$inputA'
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20 -b '$inputBs'
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21 | sort -k1,1 -k2,2n
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22 > '$output'
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
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27 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
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28 <expand macro="split" />
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29 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
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30 help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>
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31 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
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32 label="Report the depth at each position in each A feature"
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33 help="Positions reported are one based. Each position and depth follow the complete B feature (-d)" />
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34 <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""
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35 label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
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36 help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth (-hist)" />
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37 </inputs>
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38 <outputs>
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39 <data format="bed" name="output" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
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44 <param name="genome" value="coverageBedB.bed" ftype="bed" />
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45 <output name="output" file="coverageBed_result1.bed" ftype="bed" />
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46 </test>
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47 </tests>
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48 <help>
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49 <![CDATA[
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50 **What it does**
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51
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52 `bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in
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53 file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments
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54 (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest.
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55 One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that
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56 overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features.
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57 Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.
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58
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59 .. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
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61 .. class:: infomark
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62
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63 The lines in the output will be comprised of each interval in A, followed by:
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65 1. The number of features in B that overlapped (by at least one base pair) the A interval.
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66 2. The number of bases in A that had non-zero coverage from features in B.
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67 3. The length of the entry in A.
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68 4. The fraction of bases in A that had non-zero coverage from features in B.
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70 @REFERENCES@
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71 ]]>
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72 </help>
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73 <expand macro="citations" />
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74 </tool>