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comparison nucBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children 607c0576c6ab
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0:b8348686a0b9 1:82aac94b06c3
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[
9 bedtools nuc 10 bedtools nuc
10 $strand 11 $strand
11 $seq 12 $seq
12 $pattern 13 $pattern
13 $case 14 $case
14 -fi $fasta 15 -fi $fasta
15 -bed $inputA 16 -bed $input
16 &gt; $output 17 > $output
18 ]]>
17 </command> 19 </command>
18 <inputs> 20 <inputs>
19 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> 21 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
20 <param format="fasta" name="fasta" type="data" label="Fasta file"/> 22 <param format="fasta" name="fasta" type="data" label="FASTA file"/>
21 23
22 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Profile the sequence according to strand." /> 24 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
23 <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" label="Print the extracted sequence." /> 25 label="Profile the sequence according to strand" help="(-s)"/>
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)." /> 26 <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
25 <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue="" label="Igore case when matching -pattern." /> 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)"/>
26 </inputs> 32 </inputs>
27 <outputs> 33 <outputs>
28 <data format="fasta" name="output" /> 34 <data format="tabular" name="output" />
29 </outputs> 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>
30 <help> 49 <help>
31 50 <![CDATA[
32 **What it does** 51 **What it does**
33 52
34 Profiles the nucleotide content of intervals in a fasta file. 53 Profiles the nucleotide content of intervals in a fasta file.
35 54
36 @REFERENCES@ 55 @REFERENCES@
56 ]]>
37 </help> 57 </help>
38 <expand macro="citations" /> 58 <expand macro="citations" />
39 </tool> 59 </tool>