Mercurial > repos > bgruening > bedtools_test_bag
comparison shuffleBed.xml @ 12:c782e0edc4f1 draft default tip
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 19 Jun 2014 10:12:00 -0400 |
| parents | e526617a6bb9 |
| children |
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| 11:e526617a6bb9 | 12:c782e0edc4f1 |
|---|---|
| 1 <tool id="bedtools_shufflebed" name="ShuffleBed" version="0.2.0"> | 1 <tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0"> |
| 2 <description></description> | 2 <description></description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 45 <when value="True"> | 45 <when value="True"> |
| 46 <param name="incl" type="data" format="bed" label="Choose File" /> | 46 <param name="incl" type="data" format="bed" label="Choose File" /> |
| 47 </when> | 47 </when> |
| 48 </conditional> | 48 </conditional> |
| 49 | 49 |
| 50 <param name="chromfirst" type="boolean" label="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" selected="False" truevalue="-chromFirst" falsevalue="" /> | 50 <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue="" |
| 51 | 51 label="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" /> |
| 52 <param name="maxtries" type="integer" value="1000" label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" /> | 52 <param name="maxtries" type="integer" value="1000" label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" /> |
| 53 <param name="nooverlap" type="boolean" label="Don’t allow shuffled intervals to overlap" selected="False" truevalue="-noOverlapping" falsevalue="" /> | 53 <param name="nooverlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue="" label="Don’t allow shuffled intervals to overlap" /> |
| 54 <param name="allowBeyond" type="boolean" label="Allow the original the length of the original records to extebd beyond the length of the chromosome." selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" /> | 54 <param name="allowBeyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" label="Allow the original the length of the original records to extebd beyond the length of the chromosome." /> |
| 55 </inputs> | 55 </inputs> |
| 56 <outputs> | 56 <outputs> |
| 57 <data format="bed" name="output" /> | 57 <data format="bed" name="output" /> |
| 58 | |
| 59 </outputs> | 58 </outputs> |
| 60 <help> | 59 <help> |
| 61 | 60 |
| 62 **What it does** | 61 **What it does** |
| 63 | 62 |