Mercurial > repos > iuc > bedtools
annotate randomBed.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 | 607c0576c6ab |
| children | 44867b59dbf2 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.0"> |
|
4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
2
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changeset
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2 <description>generate random intervals in a genome</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 1 | 9 <![CDATA[ |
| 0 | 10 bedtools random |
| 11 -g $genome | |
| 12 -l $length | |
| 13 -n $intervals | |
| 2 | 14 #if str($seed.seed_choose) == "True": |
| 1 | 15 -seed $seed.seed |
| 0 | 16 #end if |
| 1 | 17 > "$output" |
| 18 ]]> | |
| 0 | 19 </command> |
| 20 <inputs> | |
| 21 <expand macro="genome" /> | |
| 1 | 22 <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" /> |
| 23 <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" /> | |
| 0 | 24 <expand macro="seed" /> |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <data format="bed" name="output" /> | |
| 28 </outputs> | |
| 1 | 29 <tests> |
| 30 <test> | |
| 31 <param name="genome" value="mm9_chr1.len" /> | |
| 2 | 32 <param name="seed_choose" value="False" /> |
| 1 | 33 <param name="length" value="5" /> |
| 34 <param name="intervals" value="3" /> | |
| 2 | 35 <output name="output"> |
| 36 <assert_contents> | |
| 37 <has_text_matching expression="chr1" /> | |
| 38 <has_n_columns n="6" /> | |
| 39 </assert_contents> | |
| 40 </output> | |
| 1 | 41 </test> |
| 42 </tests> | |
| 0 | 43 <help> |
| 1 | 44 <![CDATA[ |
| 0 | 45 **What it does** |
| 46 | |
| 47 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. | |
| 48 | |
| 49 @REFERENCES@ | |
| 1 | 50 ]]> |
| 0 | 51 </help> |
| 52 <expand macro="citations" /> | |
| 53 </tool> |