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comparison shuffleBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children 2cd7e321d259
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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 shuffle 10 bedtools shuffle
10 -g $genome 11 -g $genome
11 -i $inputA 12 -i $inputA
12 $bedpe 13 $bedpe
13 #if $seed.choose: 14 #if str($seed.seed_choose) == "True":
14 -seed $seed.seed 15 -seed $seed.seed
15 #end if 16 #end if
16 #if $excl.choose: 17 #if str($add_bed.add_bed_select) == "not_be":
17 -excl $excl.excl 18 -excl $add_bed_select.excl
18 -f $overlap 19 -f $add_bed_select.overlap
19 #end if 20 #elif str($add_bed.add_bed_select) == "be":
20 #if $incl.choose: 21 -incl $add_bed_select.incl
21 -incl $incl.incl
22 #end if 22 #end if
23 $chrom 23 $chrom
24 $chromfirst 24 $chromfirst
25 $nooverlap 25 $no_overlap
26 $allowBeyond 26 $allow_beyond
27 -maxTries $maxtries 27 -maxTries $maxtries
28 &gt; $output 28 > $output
29 ]]>
29 </command> 30 </command>
30 <inputs> 31 <inputs>
31 <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"/>
32 <param name="bedpe" type="boolean" label="The file is in BEDPE format" selected="False" truevalue="-bedpe" falsevalue="" /> 33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" selected="False" truevalue="-bedpe" falsevalue="" />
33 <expand macro="genome" /> 34 <expand macro="genome" />
34 <param name="chrom" type="boolean" label="Keep features in the input file on the same chromosome. Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen" selected="False" truevalue="-chrom" falsevalue="" /> 35 <param name="chrom" type="boolean" selected="False" truevalue="-chrom" falsevalue=""
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)" />
35 <expand macro="seed" /> 38 <expand macro="seed" />
36 <conditional name="excl"> 39 <conditional name="add_bed">
37 <param name="choose" type="boolean" label="Choose a BED file of coordinates in which features from -i should not be placed?" selected="False" truevalue="True" falsevalue="False" /> 40 <param name="add_bed_select" type="select" label="Choose an additional BED file">
38 <when value="True"> 41 <option value="no" selected="True">No additional BED file</option>
42 <option value="not_be">Coordinates in which features from -i should not be placed?</option>
43 <option value="be">coordinates in which features from -i should be placed?</option>
44 </param>
45 <when value="not_be">
39 <param name="excl" type="data" format="bed" label="Choose File" /> 46 <param name="excl" type="data" format="bed" label="Choose File" />
40 <expand macro="overlap" /> 47 <expand macro="overlap" />
41 </when> 48 </when>
42 </conditional> 49 <when value="be">
43 <conditional name="incl">
44 <param name="choose" type="boolean" label="Choose a BED file of coordinates in which features from -i should be placed?" selected="False" truevalue="True" falsevalue="False" />
45 <when value="True">
46 <param name="incl" type="data" format="bed" label="Choose File" /> 50 <param name="incl" type="data" format="bed" label="Choose File" />
47 </when> 51 </when>
48 </conditional> 52 </conditional>
49
50 <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue="" 53 <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue=""
51 label="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size" /> 54 label="Choose chromosome first"
52 <param name="maxtries" type="integer" value="1000" label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" /> 55 help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size. (-chromFirst)" />
53 <param name="nooverlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue="" label="Don’t allow shuffled intervals to overlap" /> 56 <param name="maxtries" type="integer" value="1000"
54 <param name="allowBeyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" label="Allow the original the length of the original records to extebd beyond the length of the chromosome." /> 57 label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" />
58 <param name="no_overlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue=""
59 label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" />
60 <param name="allow_beyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue=""
61 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" />
55 </inputs> 62 </inputs>
56 <outputs> 63 <outputs>
57 <data format="bed" name="output" /> 64 <data format="bed" name="output" />
58 </outputs> 65 </outputs>
66 <tests>
67 <test>
68 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
69 <param name="genome" value="shuffleBed.len" ftype="tabular" />
70 <param name="chrom" value="" />
71 <param name="seed_choose" value="True" />
72 <param name="seed" value="1" />
73 <output name="output" file="shuffleBed_result1.bed" ftype="bed" />
74 </test>
75 <test>
76 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
77 <param name="genome" value="shuffleBed.len" ftype="tabular" />
78 <param name="chrom" value="True" />
79 <param name="seed_choose" value="True" />
80 <param name="seed" value="1" />
81 <output name="output" file="shuffleBed_result2.bed" ftype="bed" />
82 </test>
83 <test>
84 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
85 <param name="genome" value="shuffleBed.len" ftype="tabular" />
86 <param name="excl" value="shuffleBed2.bed" ftype="bed" />
87 <param name="seed_choose" value="True" />
88 <param name="seed" value="1" />
89 <output name="output" file="shuffleBed_result3.bed" ftype="bed" />
90 </test>
91 <test>
92 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
93 <param name="genome" value="shuffleBed.len" ftype="bed" />
94 <param name="allow_beyond" value="True" />
95 <param name="seed_choose" value="True" />
96 <param name="seed" value="1" />
97 <output name="output" file="shuffleBed_result4.bed" ftype="bed" />
98 </test>
99 </tests>
59 <help> 100 <help>
60 101 <![CDATA[
61 **What it does** 102 **What it does**
62 103
63 bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” BED/GFF/VCF file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the significance of associations of one feature with another. 104 bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” BED/GFF/VCF file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the significance of associations of one feature with another.
105
64 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png 106 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png
107
65 @REFERENCES@ 108 @REFERENCES@
109 ]]>
66 </help> 110 </help>
67 <expand macro="citations" /> 111 <expand macro="citations" />
68 </tool> 112 </tool>