Mercurial > repos > iuc > bedtools
comparison shuffleBed.xml @ 10:c78cf6fe3018 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
| author | iuc |
|---|---|
| date | Mon, 03 Oct 2016 07:36:08 -0400 |
| parents | d25966c8ddeb |
| children | 7308cc546a36 |
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| 9:2ab422b551df | 10:c78cf6fe3018 |
|---|---|
| 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" selected="False" truevalue="-bedpe" falsevalue="" /> | 33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> |
| 34 <expand macro="genome" /> | 34 <expand macro="genome" /> |
| 35 <param name="chrom" type="boolean" selected="False" truevalue="-chrom" falsevalue="" | 35 <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue="" |
| 36 label="Keep features in the input file on the same chromosome" | 36 label="Keep features in the input file on the same chromosome" |
| 37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" /> | 37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" /> |
| 38 <expand macro="seed" /> | 38 <expand macro="seed" /> |
| 39 <conditional name="add_bed"> | 39 <conditional name="add_bed"> |
| 40 <param name="add_bed_select" type="select" label="Choose an additional BED file"> | 40 <param name="add_bed_select" type="select" label="Choose an additional BED file"> |
| 49 </when> | 49 </when> |
| 50 <when value="be"> | 50 <when value="be"> |
| 51 <param name="incl" type="data" format="bed" label="Choose File" /> | 51 <param name="incl" type="data" format="bed" label="Choose File" /> |
| 52 </when> | 52 </when> |
| 53 </conditional> | 53 </conditional> |
| 54 <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue="" | 54 <param name="chromfirst" type="boolean" checked="False" truevalue="-chromFirst" falsevalue="" |
| 55 label="Choose chromosome first" | 55 label="Choose chromosome first" |
| 56 help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size. (-chromFirst)" /> | 56 help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size. (-chromFirst)" /> |
| 57 <param name="maxtries" type="integer" value="1000" | 57 <param name="maxtries" type="integer" value="1000" |
| 58 label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" /> | 58 label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" /> |
| 59 <param name="no_overlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue="" | 59 <param name="no_overlap" type="boolean" checked="False" truevalue="-noOverlapping" falsevalue="" |
| 60 label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" /> | 60 label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" /> |
| 61 <param name="allow_beyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" | 61 <param name="allow_beyond" type="boolean" checked="False" truevalue="-allowBeyondChromEnd" falsevalue="" |
| 62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" /> | 62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" /> |
| 63 </inputs> | 63 </inputs> |
| 64 <outputs> | 64 <outputs> |
| 65 <data format="bed" name="output" /> | 65 <data format="bed" name="output" /> |
| 66 </outputs> | 66 </outputs> |