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annotate complementBed.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 9f6bd4c9479f
children
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64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
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1 <tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Extract intervals not represented by an interval file</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"/>
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
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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 complementBed
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11 -i '$input'
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12 @GENOME_FILE@
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13 > '$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 <expand macro="input_conditional_genome_file"/>
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18 </inputs>
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19 <outputs>
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20 <data name="output" format_source="input" metadata_source="input" label="Complement of ${input.name}"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" value="a.bed" ftype="bed"/>
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25 <param name="genome_file_opts|genome_file_opts_selector" value="hist"/>
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26 <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular"/>
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27 <output name="output" file="complementBed_result1.bed" ftype="bed"/>
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31 **What it does**
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32
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33 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input @STD_BEDTOOLS_INPUT_LABEL@ file.
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35 .. image:: $PATH_TO_IMAGES/complement-glyph.png
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37 @REFERENCES@
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38 ]]></help>
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39 <expand macro="citations"/>
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40 </tool>