Mercurial > repos > iuc > bedtools
comparison shuffleBed.xml @ 11:7308cc546a36 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
| author | iuc |
|---|---|
| date | Mon, 17 Oct 2016 10:13:35 -0400 |
| parents | c78cf6fe3018 |
| children | 44867b59dbf2 |
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| 10:c78cf6fe3018 | 11:7308cc546a36 |
|---|---|
| 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 shuffle | 10 bedtools shuffle |
| 11 -g $genome | 11 -g '$genome' |
| 12 -i $inputA | 12 -i '$inputA' |
| 13 $bedpe | 13 $bedpe |
| 14 #if str($seed.seed_choose) == "True": | 14 #if str($seed.seed_choose) == "True": |
| 15 -seed $seed.seed | 15 -seed $seed.seed |
| 16 #end if | 16 #end if |
| 17 #if str($add_bed.add_bed_select) == "not_be": | 17 #if str($add_bed.add_bed_select) == "not_be": |
| 23 $chrom | 23 $chrom |
| 24 $chromfirst | 24 $chromfirst |
| 25 $no_overlap | 25 $no_overlap |
| 26 $allow_beyond | 26 $allow_beyond |
| 27 -maxTries $maxtries | 27 -maxTries $maxtries |
| 28 > $output | 28 > '$output' |
| 29 ]]> | 29 ]]> |
| 30 </command> | 30 </command> |
| 31 <inputs> | 31 <inputs> |
| 32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | 32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> |
| 33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> | 33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> |