Mercurial > repos > iuc > bedtools
annotate slopBed.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_slopbed" name="SlopBed" 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>adjust the size of intervals</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 slop | |
| 11 $pct | |
| 12 $strand | |
| 13 -g $genome | |
| 14 -i $inputA | |
| 15 #if $addition.addition_select == 'b': | |
| 16 -b $addition.b | |
| 17 #else: | |
| 18 -l $addition.l | |
| 19 -r $addition.r | |
| 20 #end if | |
| 21 $header | |
| 22 > $output | |
| 23 ]]> | |
| 24 </command> | |
| 25 <inputs> | |
| 26 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
| 27 <expand macro="genome" /> | |
| 28 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" | |
| 29 label="Define -l and -r as a fraction of the feature’s length" | |
| 30 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" /> | |
| 31 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" | |
| 32 label="Define -l and -r based on strand" | |
| 33 help="If used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" /> | |
| 34 <expand macro="addition" /> | |
| 35 <expand macro="print_header" /> | |
| 36 </inputs> | |
| 37 <outputs> | |
| 38 <data format="bed" name="output"/> | |
| 39 </outputs> | |
| 40 <tests> | |
| 41 <test> | |
| 42 <param name="inputA" value="a.bed" ftype="bed" /> | |
| 43 <param name="genome" value="mm9_chr1.len" ftype="bed" /> | |
| 44 <param name="addition_select" value="b" /> | |
| 45 <param name="b" value="5" /> | |
| 46 <output name="output" file="slopBed_result1.bed" ftype="bed" /> | |
| 47 </test> | |
| 48 <test> | |
| 49 <param name="inputA" value="a.bed" ftype="bed" /> | |
| 50 <param name="genome" value="mm9_chr1.len" ftype="bed" /> | |
| 51 <param name="addition_select" value="lr" /> | |
| 52 <param name="l" value="2" /> | |
| 53 <param name="r" value="3" /> | |
| 54 <output name="output" file="slopBed_result2.bed" ftype="bed" /> | |
| 55 </test> | |
| 56 </tests> | |
| 57 <help> | |
| 58 <![CDATA[ | |
| 59 **What it does** | |
| 60 | |
| 61 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). | |
| 62 | |
| 63 .. image:: $PATH_TO_IMAGES/slop-glyph.png | |
| 64 | |
| 65 .. class:: warningmark | |
| 66 | |
| 67 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. | |
| 68 @REFERENCES@ | |
| 69 ]]> | |
| 70 </help> | |
| 71 <expand macro="citations" /> | |
| 72 </tool> |