Mercurial > repos > iuc > bedtools
annotate shuffleBed.xml @ 16:e0cec48a4695 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ea1ac33f3337ac44f43150f585c9ccd38e08da0c
| author | iuc |
|---|---|
| date | Fri, 18 Aug 2017 15:33:08 -0400 |
| parents | 7308cc546a36 |
| children | 44867b59dbf2 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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changeset
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2 <description>randomly redistrubute intervals in a genome</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 1 | 9 <![CDATA[ |
| 0 | 10 bedtools shuffle |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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10
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11 -g '$genome' |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
10
diff
changeset
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12 -i '$inputA' |
| 0 | 13 $bedpe |
| 1 | 14 #if str($seed.seed_choose) == "True": |
| 15 -seed $seed.seed | |
| 0 | 16 #end if |
| 1 | 17 #if str($add_bed.add_bed_select) == "not_be": |
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d25966c8ddeb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f-dirty
iuc
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4
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changeset
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18 -excl $add_bed.excl |
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d25966c8ddeb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f-dirty
iuc
parents:
4
diff
changeset
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19 -f $add_bed.overlap |
| 1 | 20 #elif str($add_bed.add_bed_select) == "be": |
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d25966c8ddeb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f-dirty
iuc
parents:
4
diff
changeset
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21 -incl $add_bed.incl |
| 0 | 22 #end if |
| 23 $chrom | |
| 24 $chromfirst | |
| 1 | 25 $no_overlap |
| 26 $allow_beyond | |
| 0 | 27 -maxTries $maxtries |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
10
diff
changeset
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28 > '$output' |
| 1 | 29 ]]> |
| 0 | 30 </command> |
| 31 <inputs> | |
| 32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
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c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents:
6
diff
changeset
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33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> |
| 0 | 34 <expand macro="genome" /> |
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10
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents:
6
diff
changeset
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35 <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue="" |
| 1 | 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)" /> | |
| 0 | 38 <expand macro="seed" /> |
| 1 | 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> | |
| 3 | 45 <when value="no" /> |
| 1 | 46 <when value="not_be"> |
| 0 | 47 <param name="excl" type="data" format="bed" label="Choose File" /> |
| 48 <expand macro="overlap" /> | |
| 49 </when> | |
| 1 | 50 <when value="be"> |
| 0 | 51 <param name="incl" type="data" format="bed" label="Choose File" /> |
| 52 </when> | |
| 53 </conditional> | |
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10
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents:
6
diff
changeset
|
54 <param name="chromfirst" type="boolean" checked="False" truevalue="-chromFirst" falsevalue="" |
| 1 | 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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10
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents:
6
diff
changeset
|
59 <param name="no_overlap" type="boolean" checked="False" truevalue="-noOverlapping" falsevalue="" |
| 1 | 60 label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" /> |
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10
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents:
6
diff
changeset
|
61 <param name="allow_beyond" type="boolean" checked="False" truevalue="-allowBeyondChromEnd" falsevalue="" |
| 1 | 62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" /> |
| 0 | 63 </inputs> |
| 64 <outputs> | |
| 65 <data format="bed" name="output" /> | |
| 66 </outputs> | |
| 1 | 67 <tests> |
| 68 <test> | |
| 69 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | |
| 70 <param name="genome" value="shuffleBed.len" ftype="tabular" /> | |
| 71 <param name="chrom" value="" /> | |
| 72 <param name="seed_choose" value="True" /> | |
| 73 <param name="seed" value="1" /> | |
| 74 <output name="output" file="shuffleBed_result1.bed" ftype="bed" /> | |
| 75 </test> | |
| 76 <test> | |
| 77 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | |
| 78 <param name="genome" value="shuffleBed.len" ftype="tabular" /> | |
| 79 <param name="chrom" value="True" /> | |
| 80 <param name="seed_choose" value="True" /> | |
| 81 <param name="seed" value="1" /> | |
| 82 <output name="output" file="shuffleBed_result2.bed" ftype="bed" /> | |
| 83 </test> | |
| 84 <test> | |
| 85 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | |
| 86 <param name="genome" value="shuffleBed.len" ftype="tabular" /> | |
| 87 <param name="excl" value="shuffleBed2.bed" ftype="bed" /> | |
| 88 <param name="seed_choose" value="True" /> | |
| 89 <param name="seed" value="1" /> | |
| 90 <output name="output" file="shuffleBed_result3.bed" ftype="bed" /> | |
| 91 </test> | |
| 92 <test> | |
| 93 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | |
| 94 <param name="genome" value="shuffleBed.len" ftype="bed" /> | |
| 95 <param name="allow_beyond" value="True" /> | |
| 96 <param name="seed_choose" value="True" /> | |
| 97 <param name="seed" value="1" /> | |
| 98 <output name="output" file="shuffleBed_result4.bed" ftype="bed" /> | |
| 99 </test> | |
| 100 </tests> | |
| 0 | 101 <help> |
| 1 | 102 <![CDATA[ |
| 0 | 103 **What it does** |
| 104 | |
| 105 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. | |
| 1 | 106 |
| 0 | 107 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png |
| 1 | 108 |
| 0 | 109 @REFERENCES@ |
| 1 | 110 ]]> |
| 0 | 111 </help> |
| 112 <expand macro="citations" /> | |
| 113 </tool> |