Mercurial > repos > iuc > bedtools

comparison coverageBed.xml @ 1:7511823bdea1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Fri, 08 Aug 2014 18:17:59 -0400
parents 4fb5ea02b441
children 315929597efb
comparison
equal deleted inserted replaced
0:4fb5ea02b441 1:7511823bdea1
1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
2 <description>of features in file A across the features in file B (coverageBed)</description> 2 <description>of features in file A across the features in file B (coverageBed)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
12 #else 12 #else
13 -a '$inputA' 13 -a '$inputA'
14 #end if 14 #end if
15 -b '$inputB' 15 -b '$inputB'
16 $d 16 $d
17 $hist
17 $split 18 $split
18 $strandedness 19 $strandedness
19 | sort -k1,1 -k2,2n 20 | sort -k1,1 -k2,2n
20 &gt; '$output' 21 &gt; '$output'
21 </command> 22 </command>
30 help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data. (-split)" /> 31 help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data. (-split)" />
31 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 32 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
32 help="That is, only features in A are only counted towards coverage in B if they are the same strand. (-s)"/> 33 help="That is, only features in A are only counted towards coverage in B if they are the same strand. (-s)"/>
33 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Report the depth at each position in each B feature" 34 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Report the depth at each position in each B feature"
34 help="Positions reported are one based. Each position and depth follow the complete B feature. (-d)" /> 35 help="Positions reported are one based. Each position and depth follow the complete B feature. (-d)" />
36 <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue="" label="Report a histogram of coverage for each feature in B as well as a summary histogram for all features in B"
37 help="Additonal columns after each feature in B: 1) depth 2) # bases at depth 3) size of B 4) % of B at depth. (-hist)" />
35 </inputs> 38 </inputs>
36 39
37 <outputs> 40 <outputs>
38 <data format="bed" name="output" metadata_source="inputB" label="count of overlaps in ${inputA.name} on ${inputB.name}"/> 41 <data format="bed" name="output" metadata_source="inputB" label="count of overlaps in ${inputA.name} on ${inputB.name}"/>
39 </outputs> 42 </outputs>
40 <help> 43 <help>
41 44
42 **What it does** 45 **What it does**
43 46
44 coverageBed_ computes both the depth and breadth of coverage of features in file A across the features in file B. For example, coverageBed can compute the coverage of sequence alignments (file A) across 1 kilobase (arbitrary) windows (file B) tiling a genome of interest. One advantage that coverageBed offers is that it not only counts the number of features that overlap an interval in file B, it also computes the fraction of bases in B interval that were overlapped by one or more features. 47 coverageBed_ computes both the depth and breadth of coverage of features in
48 file A across the features in file B. For example, coverageBed can compute the coverage of sequence alignments
49 (file A) across 1 kilobase (arbitrary) windows (file B) tiling a genome of interest.
50 One advantage that coverageBed offers is that it not only counts the number of features that
51 overlap an interval in file B, it also computes the fraction of bases in B interval that were overlapped by one or more features.
45 Thus, coverageBed also computes the breadth of coverage for each interval in B. 52 Thus, coverageBed also computes the breadth of coverage for each interval in B.
46 53
47 .. coverageBed: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html 54 .. _coverageBed: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
48 55
49 .. class:: infomark 56 .. class:: infomark
50 57
51 The output file will be comprised of each interval from your original target BED file, plus an additional column indicating the number of intervals in your source file that overlapped that target interval. 58 The output file will be comprised of each interval from your original target BED file, plus an additional column indicating the number of intervals in your source file that overlapped that target interval.
52 59
53 @REFERENCES@ 60 @REFERENCES@
54 61
55 </help> 62 </help>
63 <expand macro="citations" />
56 </tool> 64 </tool>