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1 <tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.0">
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2 <description></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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8 <command>
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9 <![CDATA[
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10 complementBed
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11 -i "$input"
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12 -g "$genome"
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13 > "$output"
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
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18 <expand macro="genome" />
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19 </inputs>
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20 <outputs>
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21 <data format_source="input" name="output" metadata_source="input" label="Complemen of ${input.name}"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input" value="a.bed" ftype="bed" />
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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>
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31 <![CDATA[
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32 **What it does**
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33
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34 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
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35
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36 .. image:: $PATH_TO_IMAGES/complement-glyph.png
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37
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38 @REFERENCES@
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39 ]]>
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40 </help>
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41 <expand macro="citations" />
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42 </tool>
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