Mercurial > repos > iuc > bedtools
annotate slopBed.xml @ 26:95a3b2c25bd1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
| author | iuc |
|---|---|
| date | Thu, 26 Apr 2018 17:02:46 -0400 |
| parents | a8eabd2838f6 |
| children | 4f7a5ccd2ae9 |
| rev | line source |
|---|---|
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
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1 <tool id="bedtools_slopbed" name="SlopBed" 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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2 <description>adjust the size of intervals</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 slop |
| 11 $pct | |
| 12 $strand | |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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11
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changeset
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13 -g @GENOME_FILE@ |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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14 -i '$inputA' |
| 0 | 15 #if $addition.addition_select == 'b': |
| 1 | 16 -b $addition.b |
| 0 | 17 #else: |
| 1 | 18 -l $addition.l |
| 19 -r $addition.r | |
| 0 | 20 #end if |
| 21 $header | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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4
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changeset
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22 > '$output' |
| 1 | 23 ]]> |
| 0 | 24 </command> |
| 25 <inputs> | |
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26
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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26 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
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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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27 <expand macro="input_conditional_genome_file" /> |
| 1 | 28 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" |
| 29 label="Define -l and -r as a fraction of the feature’s length" | |
| 30 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" /> | |
| 31 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" | |
| 32 label="Define -l and -r based on strand" | |
| 33 help="If used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" /> | |
| 0 | 34 <expand macro="addition" /> |
| 1 | 35 <expand macro="print_header" /> |
| 0 | 36 </inputs> |
| 37 <outputs> | |
| 1 | 38 <data format="bed" name="output"/> |
| 0 | 39 </outputs> |
| 1 | 40 <tests> |
| 41 <test> | |
| 42 <param name="inputA" value="a.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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43 <param name="genome_file_opts_selector" value="hist" /> |
| 1 | 44 <param name="genome" value="mm9_chr1.len" ftype="bed" /> |
| 45 <param name="addition_select" value="b" /> | |
| 46 <param name="b" value="5" /> | |
| 47 <output name="output" file="slopBed_result1.bed" ftype="bed" /> | |
| 48 </test> | |
| 49 <test> | |
| 50 <param name="inputA" value="a.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
|
51 <param name="genome_file_opts_selector" value="hist" /> |
| 1 | 52 <param name="genome" value="mm9_chr1.len" ftype="bed" /> |
| 53 <param name="addition_select" value="lr" /> | |
| 54 <param name="l" value="2" /> | |
| 55 <param name="r" value="3" /> | |
| 56 <output name="output" file="slopBed_result2.bed" ftype="bed" /> | |
| 57 </test> | |
| 58 </tests> | |
| 0 | 59 <help> |
| 1 | 60 <![CDATA[ |
| 0 | 61 **What it does** |
| 62 | |
| 63 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end > chromosome size). | |
| 64 | |
| 65 .. image:: $PATH_TO_IMAGES/slop-glyph.png | |
| 66 | |
| 67 .. class:: warningmark | |
| 68 | |
| 69 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig. | |
| 70 @REFERENCES@ | |
| 1 | 71 ]]> |
| 0 | 72 </help> |
| 73 <expand macro="citations" /> | |
| 74 </tool> |