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annotate overlapBed.xml @ 59:539958feb49c 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 11:35:06 +0000
parents 1d0a0d6a78b1
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1d0a0d6a78b1 "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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539958feb49c "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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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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9 <command><![CDATA[
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10 bedtools overlap
df28283b3778 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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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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16 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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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>