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comparison nucBed.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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1 <tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 bedtools nuc
10 $strand
11 $seq
12 $pattern
13 $case
14 -fi $fasta
15 -bed $inputA
16 &gt; $output
17 </command>
18 <inputs>
19 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
20 <param format="fasta" name="fasta" type="data" label="Fasta file"/>
21
22 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Profile the sequence according to strand." />
23 <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" label="Print the extracted sequence." />
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)." />
25 <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue="" label="Igore case when matching -pattern." />
26 </inputs>
27 <outputs>
28 <data format="fasta" name="output" />
29 </outputs>
30 <help>
31
32 **What it does**
33
34 Profiles the nucleotide content of intervals in a fasta file.
35
36 @REFERENCES@
37 </help>
38 </tool>