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annotate overlapBed.xml @ 56:7a06bb42dbb1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 07:45:56 +0000
parents df28283b3778
children 1d0a0d6a78b1
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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_overlapbed" name="bedtools OverlapBed" version="@TOOL_VERSION@">
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2 <description>computes the amount of overlap from two intervals</description>
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7a06bb42dbb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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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[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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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 $cols
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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13 > '$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>