Mercurial > repos > iuc > bedtools

comparison nucBed.xml @ 38:3f852f713d24 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
author iuc
date Sun, 21 Jan 2018 07:16:59 -0500
parents 7f4f9bb165c9
children d279800f4ff9
comparison
equal deleted inserted replaced
37:7f4f9bb165c9 38:3f852f713d24
1 <tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.1">
2 <description>profile the nucleotide content of intervals in a FASTA file</description> 2 <description>profile the nucleotide content of intervals in a FASTA file</description>
3 <macros> 3 <macros>
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 <![CDATA[
10 bedtools nuc 10 bedtools nuc
11 $strand 11 $s
12 $seq 12 $seq
13 $pattern 13 #if str($pattern):
14 $case 14 -pattern '$pattern'
15 $C
16 #end if
15 -fi '$fasta' 17 -fi '$fasta'
16 -bed '$input' 18 -bed '$input'
17 > '$output' 19 > '$output'
18 ]]> 20 ]]>
19 </command> 21 </command>
20 <inputs> 22 <inputs>
21 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> 23 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
22 <param format="fasta" name="fasta" type="data" label="FASTA file"/> 24 <param format="fasta" name="fasta" type="data" label="FASTA file"/>
23 25
24 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" 26 <param argument="-s" type="boolean" checked="false" truevalue="-s" falsevalue=""
25 label="Profile the sequence according to strand" help="(-s)"/> 27 label="Profile the sequence according to strand" />
26 <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" 28 <param argument="-seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
27 label="Print the extracted sequence" help="(-seq)"/> 29 label="Print the extracted sequence" />
28 <param name="pattern" type="boolean" checked="false" truevalue="-pattern" falsevalue="" 30 <param argument="-pattern" type="text" label="Report the number of times a user-defined sequence is observed" help="Case-sensitive by default">
29 label="Report the number of times a user-defined sequence is observed" help="case-sensitive (-pattern)" /> 31 <validator type="regex" message="Sequence should only contain letters.">^[A-Za-z]*$</validator>
30 <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue="" 32 </param>
31 label="Ignore case when matching -pattern" help="(-C)"/> 33 <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue=""
34 label="Ignore case when matching -pattern"/>
32 </inputs> 35 </inputs>
33 <outputs> 36 <outputs>
34 <data format="tabular" name="output" /> 37 <data format="tabular" name="output" />
35 </outputs> 38 </outputs>
36 <tests> 39 <tests>
43 <param name="input" value="nucBed1.bed" ftype="bed" /> 46 <param name="input" value="nucBed1.bed" ftype="bed" />
44 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> 47 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
45 <param name="seq" value="True" /> 48 <param name="seq" value="True" />
46 <output name="output" file="nucBed_result2.bed" ftype="tabular" /> 49 <output name="output" file="nucBed_result2.bed" ftype="tabular" />
47 </test> 50 </test>
51 <test>
52 <param name="input" value="nucBed1.bed" ftype="bed" />
53 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
54 <param name="seq" value="True" />
55 <param name="pattern" value="TAC" />
56 <output name="output" file="nucBed_result3.bed" ftype="tabular" />
57 </test>
48 </tests> 58 </tests>
49 <help> 59 <help>
50 <![CDATA[ 60 <![CDATA[
51 **What it does** 61 **What it does**
52 62