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comparison jaccardBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children 607c0576c6ab
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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 bedtools jaccard 10 bedtools jaccard
10 11 $strand
11 $reciprocal 12 $split
12 $strand 13 $reciprocal
13 $split 14 -f $overlap
14 -f $overlap 15 -a $inputA
15 -a $inputA 16 -b $inputB
16 -b $inputB 17 > $output
17 &gt; $output 18 ]]>
18 </command> 19 </command>
19 <inputs> 20 <inputs>
20 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> 21 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
21 <param format="bed,vcf,gff,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/> 22 <param format="bed,vcf,gff,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
22 <param name="overlap" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" /> 23 <expand macro="overlap" />
23 24 <expand macro="reciprocal" />
24 <param name="reciprocal" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B" /> 25 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
25 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue="" label="Report extract sequences in a tab-delimited format instead of in FASTA format." /> 26 label="Force strandedness"
26 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness" help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand" /> 27 help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand. (-s)" />
27 <expand macro="strand2" /> 28 <expand macro="strand2" />
29 <expand macro="split" />
28 </inputs> 30 </inputs>
29 <outputs> 31 <outputs>
30 <data format_source="inputA" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" /> 32 <data format_source="inputA" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
31 </outputs> 33 </outputs>
34 <tests>
35 <test>
36 <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
37 <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
38 <output name="output" file="jaccardBed_result1.bed" ftype="bed" />
39 </test>
40 <test>
41 <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
42 <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
43 <param name="overlap" value="0.1" />
44 <output name="output" file="jaccardBed_result2.bed" ftype="bed" />
45 </test>
46 </tests>
32 <help> 47 <help>
33 48
34 **What it does** 49 **What it does**
35 50
36 By default, bedtools jaccard reports the length of the intersection, the length of the union (minus the intersection), the final Jaccard statistic reflecting the similarity of the two sets, as well as the number of intersections. 51 By default, bedtools jaccard reports the length of the intersection, the length of the union (minus the intersection), the final Jaccard statistic reflecting the similarity of the two sets, as well as the number of intersections.