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

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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
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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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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
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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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>