Mercurial > repos > iuc > bedtools
comparison slopBed.xml @ 0:4fb5ea02b441 draft
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| author | iuc |
|---|---|
| date | Tue, 15 Jul 2014 14:42:23 -0400 |
| parents | |
| children | 7511823bdea1 |
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| -1:000000000000 | 0:4fb5ea02b441 |
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| 1 <tool id="bedtools_slopbed" name="SlopBed" 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 bedtools slop | |
| 10 $pct | |
| 11 $strand | |
| 12 -g $genome | |
| 13 -i $inputA | |
| 14 #if $addition.addition_select == 'b': | |
| 15 -b $addition.b | |
| 16 #else: | |
| 17 -l $addition.l | |
| 18 -r $addition.r | |
| 19 #end if | |
| 20 $header | |
| 21 | |
| 22 > $output | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
| 26 <expand macro="genome" /> | |
| 27 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" label="Define -l and -r as a fraction of the feature’s length" help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" /> | |
| 28 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Define -l and -r based on strand" help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" /> | |
| 29 <expand macro="addition" /> | |
| 30 <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the input file prior to results." /> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="bed" name="output" label=""/> | |
| 34 </outputs> | |
| 35 <help> | |
| 36 | |
| 37 **What it does** | |
| 38 | |
| 39 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end > chromosome size). | |
| 40 | |
| 41 .. image:: $PATH_TO_IMAGES/slop-glyph.png | |
| 42 | |
| 43 .. class:: warningmark | |
| 44 | |
| 45 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig. | |
| 46 @REFERENCES@ | |
| 47 </help> | |
| 48 </tool> |