Mercurial > repos > iuc > bedtools
annotate shuffleBed.xml @ 35:ac2040a5e6ff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
| author | iuc |
|---|---|
| date | Fri, 08 Dec 2017 03:26:23 -0500 |
| parents | b0d5e752c0c5 |
| children | d279800f4ff9 |
| rev | line source |
|---|---|
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
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changeset
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1 <tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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2 <description>randomly redistrubute intervals in a genome</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools shuffle | |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
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11 -g @GENOME_FILE@ |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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12 -i '$inputA' |
| 8 | 13 $bedpe |
| 14 #if str($seed.seed_choose) == "True": | |
| 15 -seed $seed.seed | |
| 16 #end if | |
| 17 #if str($add_bed.add_bed_select) == "not_be": | |
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ac8b17b66663
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f
iuc
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18 -excl $add_bed.excl |
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ac8b17b66663
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f
iuc
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changeset
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19 -f $add_bed.overlap |
| 8 | 20 #elif str($add_bed.add_bed_select) == "be": |
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ac8b17b66663
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f
iuc
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21 -incl $add_bed.incl |
| 8 | 22 #end if |
| 23 $chrom | |
| 24 $chromfirst | |
| 25 $no_overlap | |
| 26 $allow_beyond | |
| 27 -maxTries $maxtries | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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22
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changeset
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28 > '$output' |
| 8 | 29 ]]> |
| 30 </command> | |
| 31 <inputs> | |
| 32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
22
diff
changeset
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33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
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diff
changeset
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34 <expand macro="input_conditional_genome_file" /> |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
22
diff
changeset
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35 <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue="" |
| 8 | 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)" /> | |
| 38 <expand macro="seed" /> | |
| 39 <conditional name="add_bed"> | |
| 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> | |
| 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> | |
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bdb4509d9482
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e8e971905f5fce11a99d51b1399af45288389d76
iuc
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45 <when value="no" /> |
| 8 | 46 <when value="not_be"> |
| 47 <param name="excl" type="data" format="bed" label="Choose File" /> | |
| 48 <expand macro="overlap" /> | |
| 49 </when> | |
| 50 <when value="be"> | |
| 51 <param name="incl" type="data" format="bed" label="Choose File" /> | |
| 52 </when> | |
| 53 </conditional> | |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
22
diff
changeset
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54 <param name="chromfirst" type="boolean" checked="False" truevalue="-chromFirst" falsevalue="" |
| 8 | 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)" /> | |
| 57 <param name="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)" /> | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
22
diff
changeset
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59 <param name="no_overlap" type="boolean" checked="False" truevalue="-noOverlapping" falsevalue="" |
| 8 | 60 label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" /> |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
22
diff
changeset
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61 <param name="allow_beyond" type="boolean" checked="False" truevalue="-allowBeyondChromEnd" falsevalue="" |
| 8 | 62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" /> |
| 63 </inputs> | |
| 64 <outputs> | |
| 65 <data format="bed" name="output" /> | |
| 66 </outputs> | |
| 67 <tests> | |
| 68 <test> | |
| 69 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
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70 <param name="genome_file_opts_selector" value="hist" /> |
| 8 | 71 <param name="genome" value="shuffleBed.len" ftype="tabular" /> |
| 72 <param name="chrom" value="" /> | |
| 73 <param name="seed_choose" value="True" /> | |
| 74 <param name="seed" value="1" /> | |
| 75 <output name="output" file="shuffleBed_result1.bed" ftype="bed" /> | |
| 76 </test> | |
| 77 <test> | |
| 78 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
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79 <param name="genome_file_opts_selector" value="hist" /> |
| 8 | 80 <param name="genome" value="shuffleBed.len" ftype="tabular" /> |
| 81 <param name="chrom" value="True" /> | |
| 82 <param name="seed_choose" value="True" /> | |
| 83 <param name="seed" value="1" /> | |
| 84 <output name="output" file="shuffleBed_result2.bed" ftype="bed" /> | |
| 85 </test> | |
| 86 <test> | |
| 87 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
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88 <param name="genome_file_opts_selector" value="hist" /> |
| 8 | 89 <param name="genome" value="shuffleBed.len" ftype="tabular" /> |
| 90 <param name="excl" value="shuffleBed2.bed" ftype="bed" /> | |
| 91 <param name="seed_choose" value="True" /> | |
| 92 <param name="seed" value="1" /> | |
| 93 <output name="output" file="shuffleBed_result3.bed" ftype="bed" /> | |
| 94 </test> | |
| 95 <test> | |
| 96 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
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97 <param name="genome_file_opts_selector" value="hist" /> |
| 8 | 98 <param name="genome" value="shuffleBed.len" ftype="bed" /> |
| 99 <param name="allow_beyond" value="True" /> | |
| 100 <param name="seed_choose" value="True" /> | |
| 101 <param name="seed" value="1" /> | |
| 102 <output name="output" file="shuffleBed_result4.bed" ftype="bed" /> | |
| 103 </test> | |
| 104 </tests> | |
| 105 <help> | |
| 106 <![CDATA[ | |
| 107 **What it does** | |
| 108 | |
| 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” 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. | |
| 110 | |
| 111 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png | |
| 112 | |
| 113 @REFERENCES@ | |
| 114 ]]> | |
| 115 </help> | |
| 116 <expand macro="citations" /> | |
| 117 </tool> |