Mercurial > repos > iuc > bedtools
view nucBed.xml @ 25:e36671a0f646 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ee522a02a3fab980a5b32a1387182c951ab04968
author | iuc |
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date | Fri, 20 Apr 2018 05:30:23 -0400 |
parents | bd7721ad15aa |
children | 95a3b2c25bd1 |
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<tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.1"> <description>profile the nucleotide content of intervals in a FASTA file</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <command> <![CDATA[ bedtools nuc $s $seq #if str($pattern): -pattern '$pattern' $C #end if -fi '$fasta' -bed '$input' > '$output' ]]> </command> <inputs> <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> <param format="fasta" name="fasta" type="data" label="FASTA file"/> <param argument="-s" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Profile the sequence according to strand" /> <param argument="-seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" label="Print the extracted sequence" /> <param argument="-pattern" type="text" label="Report the number of times a user-defined sequence is observed" help="Case-sensitive by default"> <validator type="regex" message="Sequence should only contain letters.">^[A-Za-z]*$</validator> </param> <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue="" label="Ignore case when matching -pattern"/> </inputs> <outputs> <data format="tabular" name="output" /> </outputs> <tests> <test> <param name="input" value="nucBed1.bed" ftype="bed" /> <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> <output name="output" file="nucBed_result1.bed" ftype="tabular" /> </test> <test> <param name="input" value="nucBed1.bed" ftype="bed" /> <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> <param name="seq" value="True" /> <output name="output" file="nucBed_result2.bed" ftype="tabular" /> </test> <test> <param name="input" value="nucBed1.bed" ftype="bed" /> <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> <param name="seq" value="True" /> <param name="pattern" value="TAC" /> <output name="output" file="nucBed_result3.bed" ftype="tabular" /> </test> </tests> <help> <![CDATA[ **What it does** Profiles the nucleotide content of intervals in a fasta file. @REFERENCES@ ]]> </help> <expand macro="citations" /> </tool>