Mercurial > repos > iuc > bedtools
comparison randomBed.xml @ 1:82aac94b06c3 draft
Uploaded
| author | iuc |
|---|---|
| date | Thu, 08 Jan 2015 14:25:51 -0500 |
| parents | b8348686a0b9 |
| children | 457b09031d57 |
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| 0:b8348686a0b9 | 1:82aac94b06c3 |
|---|---|
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
| 8 <command> | 8 <command> |
| 9 <![CDATA[ | |
| 9 bedtools random | 10 bedtools random |
| 10 -g $genome | 11 -g $genome |
| 11 -l $length | 12 -l $length |
| 12 -n $intervals | 13 -n $intervals |
| 13 #if $seed.choose: | 14 #if $seed.seed_choose: |
| 14 -seed $seed.seed | 15 -seed $seed.seed |
| 15 #end if | 16 #end if |
| 17 > "$output" | |
| 18 ]]> | |
| 16 </command> | 19 </command> |
| 17 <inputs> | 20 <inputs> |
| 18 <expand macro="genome" /> | 21 <expand macro="genome" /> |
| 19 <param name="length" type="integer" value="100" label="The length of the intervals to generate." /> | 22 <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" /> |
| 20 <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate." /> | 23 <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" /> |
| 21 <expand macro="seed" /> | 24 <expand macro="seed" /> |
| 22 </inputs> | 25 </inputs> |
| 23 <outputs> | 26 <outputs> |
| 24 <data format="bed" name="output" /> | 27 <data format="bed" name="output" /> |
| 25 </outputs> | 28 </outputs> |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="genome" value="mm9_chr1.len" /> | |
| 32 <param name="seed_choose" value="True" /> | |
| 33 <param name="seed" value="1" /> | |
| 34 <param name="length" value="5" /> | |
| 35 <param name="intervals" value="3" /> | |
| 36 <output name="output" file="randomBed_result1.bed" ftype="bed" /> | |
| 37 </test> | |
| 38 </tests> | |
| 26 <help> | 39 <help> |
| 27 | 40 <![CDATA[ |
| 28 **What it does** | 41 **What it does** |
| 29 | 42 |
| 30 bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (-n) and the size (-l) of the intervals that should be generated. | 43 bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (-n) and the size (-l) of the intervals that should be generated. |
| 31 | 44 |
| 32 @REFERENCES@ | 45 @REFERENCES@ |
| 46 ]]> | |
| 33 </help> | 47 </help> |
| 34 <expand macro="citations" /> | 48 <expand macro="citations" /> |
| 35 </tool> | 49 </tool> |