Mercurial > repos > iuc > bedtools

annotate jaccardBed.xml @ 46:64e2edfe7a2c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
author iuc
date Sat, 18 May 2024 23:28:38 +0000
parents 7ab85ac5f64b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
39
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 35
diff changeset
1 <tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@" profile="@PROFILE@">
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
2 <description>calculate the distribution of relative distances between two files</description>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
3 <macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
4 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
5 </macros>
46
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
6 <expand macro="bio_tools"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
7 <expand macro="requirements"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
8 <expand macro="stdio"/>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
9 <command><![CDATA[
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
10 bedtools jaccard
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
11 $strand
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
12 $split
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
13 $reciprocal
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
14 @OVERLAP@
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
15 #if str($overlapB):
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
16 -F $overlapB
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
17 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
18 -a '$inputA'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
19 -b '$inputB'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
20 > '$output'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
21 ]]></command>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
22 <inputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
23 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
24 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
46
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
25 <expand macro="overlap"/>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
26 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
46
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
27 <expand macro="reciprocal"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
28 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" 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."/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
29 <expand macro="split"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
30 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
31 <outputs>
46
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
32 <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
33 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
34 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
35 <test>
46
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
36 <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
37 <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
38 <output name="output" file="jaccardBed_result1.bed" ftype="bed"/>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
39 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
40 <test>
46
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
41 <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
42 <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
43 <param name="overlap" value="0.1"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
44 <output name="output" file="jaccardBed_result2.bed" ftype="bed"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
45 </test>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
46 <test>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
47 <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
48 <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
49 <param name="overlap" value="0.1"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
50 <param name="strand" value="true"/>
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
51 <output name="output" file="jaccardBed_strand_result2.bed" ftype="bed"/>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
52 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
53 </tests>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
54 <help><![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
55 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
56
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
57 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.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
58 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.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
59
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
60 .. image:: $PATH_TO_IMAGES/jaccard-glyph.png
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
61
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
62 .. class:: warningmark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
63
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
64 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).
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
65
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
66 @REFERENCES@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
67 ]]></help>
46
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 41
diff changeset
68 <expand macro="citations"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
69 </tool>