Mercurial > repos > iuc > bedtools
annotate jaccardBed.xml @ 45:b176b1c7949e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 69394918e7a50dad3ae578e932cbac27b96e0d3b
| author | iuc |
|---|---|
| date | Tue, 24 Jul 2018 11:49:34 -0400 |
| parents | d279800f4ff9 |
| children | 2f457890d8c8 |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_jaccard" name="JaccardBed" version="@WRAPPER_VERSION@.0"> |
|
17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
|
2 <description>calculate the distribution of relative distances between two files</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 jaccard | |
| 11 $strand | |
| 12 $split | |
| 13 $reciprocal | |
| 14 -f $overlap | |
|
26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
15 -a '$inputA' |
|
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
16 -b '$inputB' |
|
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
17 > '$output' |
| 8 | 18 ]]> |
| 19 </command> | |
| 20 <inputs> | |
|
42
d279800f4ff9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents:
26
diff
changeset
|
21 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
|
d279800f4ff9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents:
26
diff
changeset
|
22 <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
| 8 | 23 <expand macro="overlap" /> |
| 24 <expand macro="reciprocal" /> | |
|
26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
25 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" |
| 8 | 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)" /> | |
| 28 <expand macro="strand2" /> | |
| 29 <expand macro="split" /> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data format_source="inputA" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" /> | |
| 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> | |
| 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> |