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comparison reldist.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 reldist 10 bedtools reldist
10 -a $inputA 11 -a $inputA
11 -b $inputB 12 -b $inputB
12 $detail 13 $detail
14 > "$output"
15 ]]>
13 </command> 16 </command>
14 <inputs> 17 <inputs>
15 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/> 18 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
16 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/> 19 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
17 <param name="detail" type="boolean" checked="false" truevalue="-detail" falsevalue="" label="Instead of a summary, report the relative distance for each interval in A" help="" /> 20 <param name="detail" type="boolean" checked="false" truevalue="-detail" falsevalue=""
21 label="Instead of a summary, report the relative distance for each interval in A" help="(-detail)" />
18 </inputs> 22 </inputs>
19 <outputs> 23 <outputs>
20 <data format_source="inputA" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}"/> 24 <data format_source="inputA" name="output" metadata_source="inputA" label="Relalative distance of ${inputA.name} and ${inputB.name}"/>
21 </outputs> 25 </outputs>
26 <tests>
27 <test>
28 <param name="inputA" value="windowBed_result1.bed" ftype="bed" />
29 <param name="inputB" value="windowBed_result1.bed" ftype="bed" />
30 <output name="output" file="reldistBed_result1.bed" ftype="bed" />
31 </test>
32 </tests>
22 <help> 33 <help>
23 34 <![CDATA[
24 **What it does** 35 **What it does**
25 36
26 Traditional approaches to summarizing the similarity between two sets of genomic intervals are based upon the number or proportion of intersecting intervals. However, such measures are largely blind to spatial correlations between the two sets where, dpesite consistent spacing or proximity, intersections are rare (for example, enhancers and transcription start sites rarely overlap, yet they are much closer to one another than two sets of random intervals). Favorov et al [1] proposed a relative distance metric that describes distribution of relative distances between each interval in one set nd the two closest intervals in another set (see figure above). If there is no spatial correlation between the two sets, one would expect the relative distances to be uniformaly distributed among the relative distances ranging from 0 to 0.5. If, however, the intervals tend to be much closer than expected by chance, the distribution of observed relative distances would be shifted towards low relative distance values (e.g., the figure below). 37 Traditional approaches to summarizing the similarity between two sets of genomic intervals are based upon the number or proportion of intersecting intervals. However, such measures are largely blind to spatial correlations between the two sets where, dpesite consistent spacing or proximity, intersections are rare (for example, enhancers and transcription start sites rarely overlap, yet they are much closer to one another than two sets of random intervals). Favorov et al proposed a relative distance metric that describes distribution of relative distances between each interval in one set nd the two closest intervals in another set (see figure above). If there is no spatial correlation between the two sets, one would expect the relative distances to be uniformaly distributed among the relative distances ranging from 0 to 0.5. If, however, the intervals tend to be much closer than expected by chance, the distribution of observed relative distances would be shifted towards low relative distance values (e.g., the figure below).
27 38
28 .. image:: $PATH_TO_IMAGES/reldist-glyph.png 39 .. image:: $PATH_TO_IMAGES/reldist-glyph.png
29 40
30 .. class:: infomark 41 .. class:: infomark
31 42
32 @REFERENCES@ 43 @REFERENCES@
33 44 ]]>
34 </help> 45 </help>
35 <expand macro="citations" /> 46 <expand macro="citations">
47 <citation type="doi">10.1371/journal.pcbi.1002529</citation>
48 </expand>
36 </tool> 49 </tool>