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annotate complementBed.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children 7a06bb42dbb1
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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_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@">
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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="requirements" />
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7 <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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8 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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9 complementBed
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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10 -i '$input'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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11 -g @GENOME_FILE@
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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12 > '$output'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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13 ]]></command>
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14 <inputs>
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15 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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16 <expand macro="input_conditional_genome_file" />
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17 </inputs>
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18 <outputs>
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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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19 <data name="output" format_source="input" metadata_source="input" label="Complement of ${input.name}"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input" value="a.bed" ftype="bed" />
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24 <param name="genome_file_opts_selector" value="hist" />
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25 <param name="genome" value="mm9_chr1.len" />
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26 <output name="output" file="complementBed_result1.bed" ftype="bed" />
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 **What it does**
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31
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32 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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34 .. image:: $PATH_TO_IMAGES/complement-glyph.png
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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>