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annotate jaccardBed.xml @ 50:df28283b3778 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 05:54:22 -0400
parents 2f457890d8c8
children 9a9f1a7abf54
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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1 <tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@+galaxy1">
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2 <description>calculate the distribution of relative distances between two files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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8 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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9 bedtools jaccard
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10 $strand
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11 $split
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12 $reciprocal
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13 @OVERLAP@
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14 #if str($overlapB):
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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15 -F $overlapB
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16 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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17 -a '$inputA'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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18 -b '$inputB'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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19 > '$output'
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20 ]]></command>
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21 <inputs>
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22 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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23 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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24 <expand macro="overlap" />
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25 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
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26 <expand macro="reciprocal" />
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27 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
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28 label="Force strandedness"
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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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." />
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30 <expand macro="strand2" />
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31 <expand macro="split" />
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32 </inputs>
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33 <outputs>
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34 <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
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39 <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
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40 <output name="output" file="jaccardBed_result1.bed" ftype="bed" />
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41 </test>
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42 <test>
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43 <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
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44 <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
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45 <param name="overlap" value="0.1" />
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46 <output name="output" file="jaccardBed_result2.bed" ftype="bed" />
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50 **What it does**
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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.
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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.
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54
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55 .. image:: $PATH_TO_IMAGES/jaccard-glyph.png
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57 .. class:: warningmark
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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).
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61 @REFERENCES@
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62 ]]></help>
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63 <expand macro="citations" />
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64 </tool>