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comparison randomBed.xml @ 17:44867b59dbf2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
author iuc
date Tue, 05 Sep 2017 15:40:14 -0400
parents 607c0576c6ab
children a8eabd2838f6
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16:e0cec48a4695 17:44867b59dbf2
1 <tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.1">
2 <description>generate random intervals in a genome</description> 2 <description>generate random intervals in a genome</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" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 bedtools random 10 bedtools random
11 -g $genome 11 -g @GENOME_FILE@
12 -l $length 12 -l $length
13 -n $intervals 13 -n $intervals
14 #if str($seed.seed_choose) == "True": 14 #if str($seed.seed_choose) == "True":
15 -seed $seed.seed 15 -seed $seed.seed
16 #end if 16 #end if
17 > "$output" 17 > "$output"
18 ]]> 18 ]]>
19 </command> 19 </command>
20 <inputs> 20 <inputs>
21 <expand macro="genome" /> 21 <expand macro="input_conditional_genome_file" />
22 <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" /> 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)" /> 23 <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" />
24 <expand macro="seed" /> 24 <expand macro="seed" />
25 </inputs> 25 </inputs>
26 <outputs> 26 <outputs>
27 <data format="bed" name="output" /> 27 <data format="bed" name="output" />
28 </outputs> 28 </outputs>
29 <tests> 29 <tests>
30 <test> 30 <test>
31 <param name="genome_file_opts_selector" value="hist" />
31 <param name="genome" value="mm9_chr1.len" /> 32 <param name="genome" value="mm9_chr1.len" />
32 <param name="seed_choose" value="False" /> 33 <param name="seed_choose" value="False" />
33 <param name="length" value="5" /> 34 <param name="length" value="5" />
34 <param name="intervals" value="3" /> 35 <param name="intervals" value="3" />
35 <output name="output"> 36 <output name="output">