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comparison randomBed.xml @ 34:dde39ba9c031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:55:48 -0400
parents 4f7a5ccd2ae9
children 3e38c9b3214f
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_randombed" name="bedtools RandomBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@">
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><![CDATA[
9 <![CDATA[ 9 bedtools random
10 bedtools random 10 -g @GENOME_FILE@
11 -g @GENOME_FILE@ 11 -l $length
12 -l $length 12 -n $intervals
13 -n $intervals 13 #if str($seed.seed_choose) == "True":
14 #if str($seed.seed_choose) == "True": 14 -seed $seed.seed
15 -seed $seed.seed 15 #end if
16 #end if 16 > '$output'
17 > "$output" 17 ]]></command>
18 ]]>
19 </command>
20 <inputs> 18 <inputs>
21 <expand macro="input_conditional_genome_file" /> 19 <expand macro="input_conditional_genome_file" />
22 <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" /> 20 <param name="length" argument="-l" type="integer" value="100" label="The length of the intervals to generate" />
23 <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" /> 21 <param name="intervals" argument="-n" type="integer" value="1000000" label="The number of intervals to generate" />
24 <expand macro="seed" /> 22 <expand macro="seed" />
25 </inputs> 23 </inputs>
26 <outputs> 24 <outputs>
27 <data format="bed" name="output" /> 25 <data name="output" format="bed" />
28 </outputs> 26 </outputs>
29 <tests> 27 <tests>
30 <test> 28 <test>
31 <param name="genome_file_opts_selector" value="hist" /> 29 <param name="genome_file_opts_selector" value="hist" />
32 <param name="genome" value="mm9_chr1.len" /> 30 <param name="genome" value="mm9_chr1.len" />
39 <has_n_columns n="6" /> 37 <has_n_columns n="6" />
40 </assert_contents> 38 </assert_contents>
41 </output> 39 </output>
42 </test> 40 </test>
43 </tests> 41 </tests>
44 <help> 42 <help><![CDATA[
45 <![CDATA[
46 **What it does** 43 **What it does**
47 44
48 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. 45 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.
49 46
50 @REFERENCES@ 47 @REFERENCES@
51 ]]> 48 ]]></help>
52 </help>
53 <expand macro="citations" /> 49 <expand macro="citations" />
54 </tool> 50 </tool>