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comparison shuffleBed.xml @ 32:b0d5e752c0c5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
author iuc
date Tue, 05 Sep 2017 09:51:56 -0400
parents c0fbce5dc84a
children ac2040a5e6ff
comparison
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31:cb98f29aa1dc 32:b0d5e752c0c5
1 <tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.1">
2 <description>randomly redistrubute intervals in a genome</description> 2 <description>randomly redistrubute 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 shuffle 10 bedtools shuffle
11 -g '$genome' 11 -g @GENOME_FILE@
12 -i '$inputA' 12 -i '$inputA'
13 $bedpe 13 $bedpe
14 #if str($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
29 ]]> 29 ]]>
30 </command> 30 </command>
31 <inputs> 31 <inputs>
32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> 32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> 33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" />
34 <expand macro="genome" /> 34 <expand macro="input_conditional_genome_file" />
35 <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue="" 35 <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue=""
36 label="Keep features in the input file on the same chromosome" 36 label="Keep features in the input file on the same chromosome"
37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" /> 37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" />
38 <expand macro="seed" /> 38 <expand macro="seed" />
39 <conditional name="add_bed"> 39 <conditional name="add_bed">
65 <data format="bed" name="output" /> 65 <data format="bed" name="output" />
66 </outputs> 66 </outputs>
67 <tests> 67 <tests>
68 <test> 68 <test>
69 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> 69 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
70 <param name="genome_file_opts_selector" value="hist" />
70 <param name="genome" value="shuffleBed.len" ftype="tabular" /> 71 <param name="genome" value="shuffleBed.len" ftype="tabular" />
71 <param name="chrom" value="" /> 72 <param name="chrom" value="" />
72 <param name="seed_choose" value="True" /> 73 <param name="seed_choose" value="True" />
73 <param name="seed" value="1" /> 74 <param name="seed" value="1" />
74 <output name="output" file="shuffleBed_result1.bed" ftype="bed" /> 75 <output name="output" file="shuffleBed_result1.bed" ftype="bed" />
75 </test> 76 </test>
76 <test> 77 <test>
77 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> 78 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
79 <param name="genome_file_opts_selector" value="hist" />
78 <param name="genome" value="shuffleBed.len" ftype="tabular" /> 80 <param name="genome" value="shuffleBed.len" ftype="tabular" />
79 <param name="chrom" value="True" /> 81 <param name="chrom" value="True" />
80 <param name="seed_choose" value="True" /> 82 <param name="seed_choose" value="True" />
81 <param name="seed" value="1" /> 83 <param name="seed" value="1" />
82 <output name="output" file="shuffleBed_result2.bed" ftype="bed" /> 84 <output name="output" file="shuffleBed_result2.bed" ftype="bed" />
83 </test> 85 </test>
84 <test> 86 <test>
85 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> 87 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
88 <param name="genome_file_opts_selector" value="hist" />
86 <param name="genome" value="shuffleBed.len" ftype="tabular" /> 89 <param name="genome" value="shuffleBed.len" ftype="tabular" />
87 <param name="excl" value="shuffleBed2.bed" ftype="bed" /> 90 <param name="excl" value="shuffleBed2.bed" ftype="bed" />
88 <param name="seed_choose" value="True" /> 91 <param name="seed_choose" value="True" />
89 <param name="seed" value="1" /> 92 <param name="seed" value="1" />
90 <output name="output" file="shuffleBed_result3.bed" ftype="bed" /> 93 <output name="output" file="shuffleBed_result3.bed" ftype="bed" />
91 </test> 94 </test>
92 <test> 95 <test>
93 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> 96 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
97 <param name="genome_file_opts_selector" value="hist" />
94 <param name="genome" value="shuffleBed.len" ftype="bed" /> 98 <param name="genome" value="shuffleBed.len" ftype="bed" />
95 <param name="allow_beyond" value="True" /> 99 <param name="allow_beyond" value="True" />
96 <param name="seed_choose" value="True" /> 100 <param name="seed_choose" value="True" />
97 <param name="seed" value="1" /> 101 <param name="seed" value="1" />
98 <output name="output" file="shuffleBed_result4.bed" ftype="bed" /> 102 <output name="output" file="shuffleBed_result4.bed" ftype="bed" />