Mercurial > repos > iuc > bedtools
annotate shuffleBed.xml @ 32:4f7a5ccd2ae9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
| author | iuc |
|---|---|
| date | Tue, 11 Dec 2018 14:01:26 -0500 |
| parents | 95a3b2c25bd1 |
| children | dde39ba9c031 |
| rev | line source |
|---|---|
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32
4f7a5ccd2ae9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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changeset
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1 <tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@WRAPPER_VERSION@"> |
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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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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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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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11 -g @GENOME_FILE@ |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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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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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
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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
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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 $maxtries |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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diff
changeset
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28 > '$output' |
| 1 | 29 ]]> |
| 0 | 30 </command> |
| 31 <inputs> | |
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95a3b2c25bd1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
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32 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
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c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents:
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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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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
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changeset
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34 <expand macro="input_conditional_genome_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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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
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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
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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
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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" /> | |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
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70 <param name="genome_file_opts_selector" value="hist" /> |
| 1 | 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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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
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79 <param name="genome_file_opts_selector" value="hist" /> |
| 1 | 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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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
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88 <param name="genome_file_opts_selector" value="hist" /> |
| 1 | 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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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
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97 <param name="genome_file_opts_selector" value="hist" /> |
| 1 | 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> | |
| 0 | 105 <help> |
| 1 | 106 <![CDATA[ |
| 0 | 107 **What it does** |
| 108 | |
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95a3b2c25bd1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents:
19
diff
changeset
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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. |
| 1 | 110 |
| 0 | 111 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png |
| 1 | 112 |
| 0 | 113 @REFERENCES@ |
| 1 | 114 ]]> |
| 0 | 115 </help> |
| 116 <expand macro="citations" /> | |
| 117 </tool> |