Mercurial > repos > iuc > bedtools
annotate reldist.xml @ 36:1133660b0f9d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a
| author | iuc |
|---|---|
| date | Wed, 10 Jan 2018 19:21:14 -0500 |
| parents | ac2040a5e6ff |
| children | d279800f4ff9 |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_reldistbed" name="ReldistBed" version="@WRAPPER_VERSION@.0"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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2 <description>calculate the distribution of relative distances</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools reldist | |
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f0aca67fdb71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377
iuc
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11 -a '$inputA' |
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f0aca67fdb71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377
iuc
parents:
17
diff
changeset
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12 -b '$inputB' |
| 8 | 13 $detail |
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28
f0aca67fdb71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377
iuc
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17
diff
changeset
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14 > '$output' |
| 8 | 15 ]]> |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/> | |
| 19 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/> | |
| 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)" /> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format_source="inputA" name="output" metadata_source="inputA" label="Relalative distance of ${inputA.name} and ${inputB.name}"/> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
28
diff
changeset
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28 <param name="inputA" value="a.bed" ftype="bed" /> |
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
28
diff
changeset
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29 <param name="inputB" value="a.bed" ftype="bed" /> |
| 8 | 30 <output name="output" file="reldistBed_result1.bed" ftype="bed" /> |
| 31 </test> | |
| 32 </tests> | |
| 33 <help> | |
| 34 <![CDATA[ | |
| 35 **What it does** | |
| 36 | |
| 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). | |
| 38 | |
| 39 .. image:: $PATH_TO_IMAGES/reldist-glyph.png | |
| 40 | |
| 41 .. class:: infomark | |
| 42 | |
| 43 @REFERENCES@ | |
| 44 ]]> | |
| 45 </help> | |
| 46 <expand macro="citations"> | |
| 47 <citation type="doi">10.1371/journal.pcbi.1002529</citation> | |
| 48 </expand> | |
| 49 </tool> |