Mercurial > repos > iuc > bedtools
annotate jaccardBed.xml @ 16:e0cec48a4695 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ea1ac33f3337ac44f43150f585c9ccd38e08da0c
| author | iuc |
|---|---|
| date | Fri, 18 Aug 2017 15:33:08 -0400 |
| parents | 7308cc546a36 |
| children | 95a3b2c25bd1 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bedtools_jaccard" name="JaccardBed" version="@WRAPPER_VERSION@.0"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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changeset
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2 <description>calculate the distribution of relative distances between two files</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 1 | 9 <![CDATA[ |
| 0 | 10 bedtools jaccard |
| 1 | 11 $strand |
| 12 $split | |
| 13 $reciprocal | |
| 14 -f $overlap | |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
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15 -a '$inputA' |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
16 -b '$inputB' |
|
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
17 > '$output' |
| 1 | 18 ]]> |
| 0 | 19 </command> |
| 20 <inputs> | |
| 21 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
| 22 <param format="bed,vcf,gff,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/> | |
| 1 | 23 <expand macro="overlap" /> |
| 24 <expand macro="reciprocal" /> | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
25 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" |
| 1 | 26 label="Force strandedness" |
| 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)" /> | |
| 0 | 28 <expand macro="strand2" /> |
| 1 | 29 <expand macro="split" /> |
| 0 | 30 </inputs> |
| 31 <outputs> | |
| 32 <data format_source="inputA" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" /> | |
| 33 </outputs> | |
| 1 | 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> | |
| 0 | 47 <help> |
| 48 | |
| 49 **What it does** | |
| 50 | |
| 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. | |
| 52 Whereas the bedtools intersect tool enumerates each an every intersection between two sets of genomic intervals, one often needs a single statistic reflecting the similarity of the two sets based on the intersections between them. The Jaccard statistic is used in set theory to represent the ratio of the intersection of two sets to the union of the two sets. Similarly, Favorov et al [1] reported the use of the Jaccard statistic for genome intervals: specifically, it measures the ratio of the number of intersecting base pairs between two sets to the number of base pairs in the union of the two sets. The bedtools jaccard tool implements this statistic, yet modifies the statistic such that the length of the intersection is subtracted from the length of the union. As a result, the final statistic ranges from 0.0 to 1.0, where 0.0 represents no overlap and 1.0 represent complete overlap. | |
| 53 | |
| 54 .. image:: $PATH_TO_IMAGES/jaccard-glyph.png | |
| 55 | |
| 56 .. class:: warningmark | |
| 57 | |
| 58 The jaccard tool requires that your data is pre-sorted by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files). | |
| 59 | |
| 60 @REFERENCES@ | |
| 61 </help> | |
| 62 <expand macro="citations" /> | |
| 63 </tool> |