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1 <tool id="bedtools_nucbed" name="NucBed" 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 bedtools nuc
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10 $strand
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11 $seq
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12 $pattern
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13 $case
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14 -fi $fasta
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15 -bed $inputA
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16 > $output
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17 </command>
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18 <inputs>
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19 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
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20 <param format="fasta" name="fasta" type="data" label="Fasta file"/>
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21
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22 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Profile the sequence according to strand." />
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23 <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" label="Print the extracted sequence." />
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24 <param name="pattern" type="boolean" checked="false" truevalue="-pattern" falsevalue="" label="Report the number of times a user-defined sequence is observed (case-sensitive)." />
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25 <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue="" label="Igore case when matching -pattern." />
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26 </inputs>
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27 <outputs>
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28 <data format="fasta" name="output" />
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29 </outputs>
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30 <help>
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31
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32 **What it does**
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33
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34 Profiles the nucleotide content of intervals in a fasta file.
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35
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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>
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