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annotate overlapBed.xml @ 41:7ab85ac5f64b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
author iuc
date Thu, 04 Nov 2021 11:36:55 +0000
parents 3e38c9b3214f
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3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>computes the amount of overlap from two intervals</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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7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
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6 <expand macro="bio_tools" />
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 bedtools overlap
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11 -i '$input'
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12 -cols $cols
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13 > '$output'
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14 ]]></command>
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15 <inputs>
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16 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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17 <param name="cols" type="data_column" data_ref="input" multiple="true"
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18 label="Specify the columns for the starts and ends of the features for which you’d like to compute the overlap/distance"
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19 help="The columns must be listed in the following order: start1,end1,start2,end2" />
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20 </inputs>
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21 <outputs>
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22 <data name="output" format_source="input" metadata_source="input" label="Overlap of ${input.name}"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="windowBed_result1.bed" ftype="bed" />
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27 <param name="cols" value="2,3,5,6" />
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28 <output name="output" file="overlapBed_result1.bed" ftype="bed" />
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29 </test>
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30 </tests>
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31 <help><![CDATA[
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32 **What it does**
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34 overlap computes the amount of overlap (in the case of positive values) or distance (in the case of negative values) between feature coordinates occurring on the same input line and reports the result at the end of the same line. In this way, it is a useful method for computing custom overlap scores from the output of other BEDTools.
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36 @REFERENCES@
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37 ]]></help>
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38 <expand macro="citations" />
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39 </tool>