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comparison jaccardBed.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 539958feb49c
children
comparison
equal deleted inserted replaced
63:7411007544bf 64:f6c88d2e9ae5
1 <tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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="bio_tools" /> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements" /> 7 <expand macro="requirements"/>
8 <expand macro="stdio" /> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 bedtools jaccard 10 bedtools jaccard
11 $strand 11 $strand
12 $split 12 $split
13 $reciprocal 13 $reciprocal
20 > '$output' 20 > '$output'
21 ]]></command> 21 ]]></command>
22 <inputs> 22 <inputs>
23 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 23 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
24 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 24 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
25 <expand macro="overlap" /> 25 <expand macro="overlap"/>
26 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/> 26 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
27 <expand macro="reciprocal" /> 27 <expand macro="reciprocal"/>
28 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" 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."/>
29 label="Force strandedness" 29 <expand macro="split"/>
30 help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand." />
31 <expand macro="strand2" />
32 <expand macro="split" />
33 </inputs> 30 </inputs>
34 <outputs> 31 <outputs>
35 <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" /> 32 <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}"/>
36 </outputs> 33 </outputs>
37 <tests> 34 <tests>
38 <test> 35 <test>
39 <param name="inputA" value="jaccardBed1.bed" ftype="bed" /> 36 <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
40 <param name="inputB" value="jaccardBed2.bed" ftype="bed" /> 37 <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
41 <output name="output" file="jaccardBed_result1.bed" ftype="bed" /> 38 <output name="output" file="jaccardBed_result1.bed" ftype="bed"/>
42 </test> 39 </test>
43 <test> 40 <test>
44 <param name="inputA" value="jaccardBed1.bed" ftype="bed" /> 41 <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
45 <param name="inputB" value="jaccardBed2.bed" ftype="bed" /> 42 <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
46 <param name="overlap" value="0.1" /> 43 <param name="overlap" value="0.1"/>
47 <output name="output" file="jaccardBed_result2.bed" ftype="bed" /> 44 <output name="output" file="jaccardBed_result2.bed" ftype="bed"/>
45 </test>
46 <test>
47 <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
48 <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
49 <param name="overlap" value="0.1"/>
50 <param name="strand" value="true"/>
51 <output name="output" file="jaccardBed_strand_result2.bed" ftype="bed"/>
48 </test> 52 </test>
49 </tests> 53 </tests>
50 <help><![CDATA[ 54 <help><![CDATA[
51 **What it does** 55 **What it does**
52 56
59 63
60 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). 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).
61 65
62 @REFERENCES@ 66 @REFERENCES@
63 ]]></help> 67 ]]></help>
64 <expand macro="citations" /> 68 <expand macro="citations"/>
65 </tool> 69 </tool>