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comparison nucBed.xml @ 10:71af3ebbbb7a draft

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author iuc
date Wed, 29 Apr 2015 12:06:53 -0400
parents 0d3aa592ce27
children a2d4c30ba2f9
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9:21f1d1c5467b 10:71af3ebbbb7a
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 <![CDATA[
10 bedtools nuc
11 $strand
12 $seq
13 $pattern
14 $case
15 -fi $fasta
16 -bed $input
17 > $output
18 ]]>
19 </command>
20 <inputs>
21 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
22 <param format="fasta" name="fasta" type="data" label="FASTA file"/>
23
24 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
25 label="Profile the sequence according to strand" help="(-s)"/>
26 <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
27 label="Print the extracted sequence" help="(-seq)"/>
28 <param name="pattern" type="boolean" checked="false" truevalue="-pattern" falsevalue=""
29 label="Report the number of times a user-defined sequence is observed" help="case-sensitive (-pattern)" />
30 <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue=""
31 label="Igore case when matching -pattern" help="(-C)"/>
32 </inputs>
33 <outputs>
34 <data format="tabular" name="output" />
35 </outputs>
36 <tests>
37 <test>
38 <param name="input" value="nucBed1.bed" ftype="bed" />
39 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
40 <output name="output" file="nucBed_result1.bed" ftype="tabular" />
41 </test>
42 <test>
43 <param name="input" value="nucBed1.bed" ftype="bed" />
44 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
45 <param name="seq" value="True" />
46 <output name="output" file="nucBed_result2.bed" ftype="tabular" />
47 </test>
48 </tests>
49 <help>
50 <![CDATA[
51 **What it does**
52
53 Profiles the nucleotide content of intervals in a fasta file.
54
55 @REFERENCES@
56 ]]>
57 </help>
58 <expand macro="citations" />
59 </tool>