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comparison coverageBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children d25966c8ddeb
comparison
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0:b8348686a0b9 1:82aac94b06c3
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[
9 coverageBed 10 coverageBed
10 #if $inputA.ext == "bam" 11 #if $inputA.ext == "bam"
11 -abam '$inputA' 12 -abam '$inputA'
12 #else 13 #else
13 -a '$inputA' 14 -a '$inputA'
16 $d 17 $d
17 $hist 18 $hist
18 $split 19 $split
19 $strandedness 20 $strandedness
20 | sort -k1,1 -k2,2n 21 | sort -k1,1 -k2,2n
21 &gt; '$output' 22 > '$output'
23 ]]>
22 </command> 24 </command>
23 <inputs> 25 <inputs>
24 <param format="bed,bam,gff,gg3,vcf" name="inputA" type="data" label="Count how many intervals in this BED/VCF/GFF/BAM file (source)"> 26 <param format="bed,bam,gff,gg3,vcf" name="inputA" type="data" label="Count how many intervals in this BED/VCF/GFF/BAM file (source)" />
25 <validator type="unspecified_build" /> 27 <param format="bed,gff,gff3,vcf" name="inputB" type="data" label="overlap the intervals in this BED file (target)" />
26 </param> 28 <expand macro="split" />
27 <param format="bed,gff,gff3,vcf" name="inputB" type="data" label="overlap the intervals in this BED file (target)">
28 <validator type="unspecified_build" />
29 </param>
30 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage"
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)" />
32 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 29 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
33 help="That is, only features in A are only counted towards coverage in B if they are the same strand. (-s)"/> 30 help="That is, only features in A are only counted towards coverage in B if they are the same strand. (-s)"/>
34 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Report the depth at each position in each B feature" 31 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
32 label="Report the depth at each position in each B feature"
35 help="Positions reported are one based. Each position and depth follow the complete B feature. (-d)" /> 33 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" 34 <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""
35 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)" /> 36 help="Additonal columns after each feature in B: 1) depth 2) # bases at depth 3) size of B 4) % of B at depth. (-hist)" />
38 </inputs> 37 </inputs>
39
40 <outputs> 38 <outputs>
41 <data format="bed" name="output" metadata_source="inputB" label="count of overlaps in ${inputA.name} on ${inputB.name}"/> 39 <data format="bed" name="output" metadata_source="inputB" label="Count of overlaps in ${inputA.name} on ${inputB.name}"/>
42 </outputs> 40 </outputs>
41 <tests>
42 <test>
43 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
44 <param name="genome" value="coverageBedB.bed" ftype="bed" />
45 <output name="output" file="coverageBed_result1.bed" ftype="bed" />
46 </test>
47 </tests>
43 <help> 48 <help>
44 49 <![CDATA[
45 **What it does** 50 **What it does**
46 51
47 coverageBed_ computes both the depth and breadth of coverage of features in 52 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 53 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. 54 (file A) across 1 kilobase (arbitrary) windows (file B) tiling a genome of interest.
56 .. class:: infomark 61 .. class:: infomark
57 62
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. 63 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.
59 64
60 @REFERENCES@ 65 @REFERENCES@
61 66 ]]>
62 </help> 67 </help>
63 <expand macro="citations" /> 68 <expand macro="citations" />
64 </tool> 69 </tool>