Mercurial > repos > iuc > bedtools
annotate nucBed.xml @ 17:a2d4c30ba2f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
| author | iuc |
|---|---|
| date | Sun, 21 Jun 2015 22:49:46 -0400 |
| parents | 0d3aa592ce27 |
| children | c0fbce5dc84a |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0"> |
|
17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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2 <description>profile the nucleotide content of intervals in a FASTA file</description> |
| 8 | 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> |