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comparison jaccardBed.xml @ 34:dde39ba9c031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:55:48 -0400
parents 4f7a5ccd2ae9
children b28e0cfa7ba1
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@+galaxy1">
2 <description>calculate the distribution of relative distances between two files</description> 2 <description>calculate the distribution of relative distances between two files</description>
3 <macros> 3 <macros>
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><![CDATA[
9 <![CDATA[ 9 bedtools jaccard
10 bedtools jaccard 10 $strand
11 $strand 11 $split
12 $split 12 $reciprocal
13 $reciprocal 13 @OVERLAP@
14 -f $overlap 14 #if str($overlapB):
15 -a '$inputA' 15 -F $overlapB
16 -b '$inputB' 16 #end if
17 > '$output' 17 -a '$inputA'
18 ]]> 18 -b '$inputB'
19 </command> 19 > '$output'
20 ]]></command>
20 <inputs> 21 <inputs>
21 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 22 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
22 <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 23 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
23 <expand macro="overlap" /> 24 <expand macro="overlap" />
25 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
24 <expand macro="reciprocal" /> 26 <expand macro="reciprocal" />
25 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" 27 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
26 label="Force strandedness" 28 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)" /> 29 help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand." />
28 <expand macro="strand2" /> 30 <expand macro="strand2" />
29 <expand macro="split" /> 31 <expand macro="split" />
30 </inputs> 32 </inputs>
31 <outputs> 33 <outputs>
32 <data format_source="inputA" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" /> 34 <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
33 </outputs> 35 </outputs>
34 <tests> 36 <tests>
35 <test> 37 <test>
36 <param name="inputA" value="jaccardBed1.bed" ftype="bed" /> 38 <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
37 <param name="inputB" value="jaccardBed2.bed" ftype="bed" /> 39 <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
42 <param name="inputB" value="jaccardBed2.bed" ftype="bed" /> 44 <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
43 <param name="overlap" value="0.1" /> 45 <param name="overlap" value="0.1" />
44 <output name="output" file="jaccardBed_result2.bed" ftype="bed" /> 46 <output name="output" file="jaccardBed_result2.bed" ftype="bed" />
45 </test> 47 </test>
46 </tests> 48 </tests>
47 <help> 49 <help><![CDATA[
48
49 **What it does** 50 **What it does**
50 51
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 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 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
56 .. class:: warningmark 57 .. class:: warningmark
57 58
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 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
60 @REFERENCES@ 61 @REFERENCES@
61 </help> 62 ]]></help>
62 <expand macro="citations" /> 63 <expand macro="citations" />
63 </tool> 64 </tool>