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comparison shuffleBed.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 ce3c7f062223
comparison
equal deleted inserted replaced
33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@">
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><![CDATA[
9 <![CDATA[ 9 bedtools shuffle
10 bedtools shuffle 10 -g @GENOME_FILE@
11 -g @GENOME_FILE@ 11 -i '$inputA'
12 -i '$inputA' 12 $bedpe
13 $bedpe 13 #if str($seed.seed_choose) == "True":
14 #if str($seed.seed_choose) == "True": 14 -seed $seed.seed
15 -seed $seed.seed 15 #end if
16 #end if 16 #if str($add_bed.add_bed_select) == "not_be":
17 #if str($add_bed.add_bed_select) == "not_be": 17 -excl $add_bed.excl
18 -excl $add_bed.excl 18 #if str($add_bed.overlap)
19 -f $add_bed.overlap 19 -f $add_bed.overlap
20 #elif str($add_bed.add_bed_select) == "be": 20 #end if
21 -incl $add_bed.incl 21 #elif str($add_bed.add_bed_select) == "be":
22 #end if 22 -incl $add_bed.incl
23 $chrom 23 #end if
24 $chromfirst 24 $chrom
25 $no_overlap 25 $chromfirst
26 $allow_beyond 26 $no_overlap
27 -maxTries $maxtries 27 $allow_beyond
28 > '$output' 28 -maxTries $maxtries
29 ]]> 29 > '$output'
30 </command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 32 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> 33 <param argument="-bedpe" type="boolean" truevalue="-bedpe" falsevalue="" checked="false" label="The file is in BEDPE format" />
34 <expand macro="input_conditional_genome_file" /> 34 <expand macro="input_conditional_genome_file" />
35 <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue="" 35 <param argument="-chrom" type="boolean" truevalue="-chrom" falsevalue="" checked="false"
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." />
38 <expand macro="seed" /> 38 <expand macro="seed" />
39 <conditional name="add_bed"> 39 <conditional name="add_bed">
40 <param name="add_bed_select" type="select" label="Choose an additional BED file"> 40 <param name="add_bed_select" type="select" label="Choose an additional BED file">
41 <option value="no" selected="True">No additional BED file</option> 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> 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> 43 <option value="be">coordinates in which features from -i should be placed?</option>
44 </param> 44 </param>
45 <when value="no" /> 45 <when value="no" />
46 <when value="not_be"> 46 <when value="not_be">
47 <param name="excl" type="data" format="bed" label="Choose File" /> 47 <param argument="-excl" type="data" format="bed" label="Choose File" />
48 <expand macro="overlap" /> 48 <expand macro="fraction" name="overlap" argument="-f" label="Maximum overlap (as a fraction of the -i feature) with an -excl feature that is tolerated before searching for a new, randomized locus" />
49 </when> 49 </when>
50 <when value="be"> 50 <when value="be">
51 <param name="incl" type="data" format="bed" label="Choose File" /> 51 <param argument="-incl" type="data" format="bed" label="Choose File" />
52 </when> 52 </when>
53 </conditional> 53 </conditional>
54 <param name="chromfirst" type="boolean" checked="False" truevalue="-chromFirst" falsevalue="" 54 <param name="chromfirst" argument="-chromFirst" type="boolean" truevalue="-chromFirst" falsevalue="" checked="false"
55 label="Choose chromosome first" 55 label="Choose chromosome first"
56 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)" /> 56 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." />
57 <param name="maxtries" type="integer" value="1000" 57 <param name="maxtries" argument="-maxTries" type="integer" value="1000"
58 label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" /> 58 label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" />
59 <param name="no_overlap" type="boolean" checked="False" truevalue="-noOverlapping" falsevalue="" 59 <param name="no_overlap" argument="-noOverlapping" type="boolean" truevalue="-noOverlapping" falsevalue="" checked="false"
60 label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" /> 60 label="Don’t allow shuffled intervals to overlap" />
61 <param name="allow_beyond" type="boolean" checked="False" truevalue="-allowBeyondChromEnd" falsevalue="" 61 <param name="allow_beyond" argument="-allowBeyondChromEnd" type="boolean" truevalue="-allowBeyondChromEnd" falsevalue="" checked="false"
62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" /> 62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" />
63 </inputs> 63 </inputs>
64 <outputs> 64 <outputs>
65 <data format="bed" name="output" /> 65 <data name="output" format="bed" />
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_file_opts_selector" value="hist" />
100 <param name="seed_choose" value="True" /> 100 <param name="seed_choose" value="True" />
101 <param name="seed" value="1" /> 101 <param name="seed" value="1" />
102 <output name="output" file="shuffleBed_result4.bed" ftype="bed" /> 102 <output name="output" file="shuffleBed_result4.bed" ftype="bed" />
103 </test> 103 </test>
104 </tests> 104 </tests>
105 <help> 105 <help><![CDATA[
106 <![CDATA[
107 **What it does** 106 **What it does**
108 107
109 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” @STD_BEDTOOLS_INPUT_LABEL@ 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. 108 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” @STD_BEDTOOLS_INPUT_LABEL@ 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.
110 109
111 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png 110 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png
112 111
113 @REFERENCES@ 112 @REFERENCES@
114 ]]> 113 ]]></help>
115 </help>
116 <expand macro="citations" /> 114 <expand macro="citations" />
117 </tool> 115 </tool>