Mercurial > repos > iuc > bedtools

annotate complementBed.xml @ 40:a68aa6c1204a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 29bd1be4655cd26052095a49a8e188d2572b703b"
author iuc
date Thu, 09 Sep 2021 13:04:07 +0000
parents 3e38c9b3214f
children 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_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>Extract intervals not represented by an interval file</description>
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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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9 <command><![CDATA[
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10 complementBed
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11 -i '$input'
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12 -g @GENOME_FILE@
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13 > '$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_selector" value="hist" />
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26 <param name="genome" value="mm9_chr1.len" />
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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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36
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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>