Mercurial > repos > iuc > bedtools
annotate flankBed.xml @ 30:db1841942d2b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b67e138b17f7e8cb34f59bed0925f691ec9740f3
| author | iuc |
|---|---|
| date | Fri, 17 Aug 2018 05:42:39 -0400 |
| parents | 95a3b2c25bd1 |
| 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_flankbed" name="FlankBed" 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>create new intervals from the flanks of existing intervals</description> |
| 1 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 flankBed | |
| 11 $pct | |
| 12 $strand | |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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13 -g @GENOME_FILE@ |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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14 -i '$input' |
| 1 | 15 |
| 16 #if $addition.addition_select == 'b': | |
| 17 -b $addition.b | |
| 18 #else: | |
| 19 -l $addition.l | |
| 20 -r $addition.r | |
| 21 #end if | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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4
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changeset
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22 > '$output' |
| 1 | 23 ]]> |
| 24 </command> | |
| 25 <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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19
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changeset
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26 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
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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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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" | |
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4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
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30 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. (-pct)" /> |
| 1 | 31 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" |
| 32 label="Define -l and -r based on strand" | |
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4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
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33 help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate. (-s)" /> |
| 1 | 34 <expand macro="addition" /> |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data metadata_source="input" format_source="input" name="output" /> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 <test> | |
| 41 <param name="input" 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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42 <param name="genome_file_opts_selector" value="hist" /> |
| 1 | 43 <param name="genome" value="mm9_chr1.len"/> |
| 44 <param name="addition_select" value="b"/> | |
| 45 <param name="b" value="5"/> | |
| 46 <output name="output" file="flankBed_result1.bed" ftype="bed" /> | |
| 47 </test> | |
| 48 <test> | |
| 49 <param name="input" 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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50 <param name="genome_file_opts_selector" value="hist" /> |
| 1 | 51 <param name="genome" value="mm9_chr1.len"/> |
| 52 <param name="addition_select" value="lr"/> | |
| 53 <param name="l" value="2"/> | |
| 54 <param name="r" value="3"/> | |
| 55 <output name="output" file="flankBed_result2.bed" ftype="bed" /> | |
| 56 </test> | |
| 57 </tests> | |
| 58 <help> | |
| 59 <![CDATA[ | |
| 60 **What it does** | |
| 61 | |
| 62 bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval. | |
| 63 | |
| 64 .. image:: $PATH_TO_IMAGES/flank-glyph.png | |
| 65 | |
| 66 .. class:: warningmark | |
| 67 | |
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db1841942d2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b67e138b17f7e8cb34f59bed0925f691ec9740f3
iuc
parents:
26
diff
changeset
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68 In order to prevent creating intervals that violate chromosome boundaries, bedTools flank requires a bedTool genome file defining the length of each chromosome or contig. . This should be a two column tabular file with the chromosome name in the first column and the END coordinate of the chromosome in the second column. |
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db1841942d2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b67e138b17f7e8cb34f59bed0925f691ec9740f3
iuc
parents:
26
diff
changeset
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69 |
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db1841942d2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b67e138b17f7e8cb34f59bed0925f691ec9740f3
iuc
parents:
26
diff
changeset
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70 If you need this data for any genome that is at UCSC (http://genome.ucsc.edu), it can be extracted from the Table Browser with the "Get Data: UCSC Main" tool. Set "group" to "All Tables", "table" to "chromInfo", and "output format" to "all fields from selected table". |
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db1841942d2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b67e138b17f7e8cb34f59bed0925f691ec9740f3
iuc
parents:
26
diff
changeset
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71 |
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db1841942d2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b67e138b17f7e8cb34f59bed0925f691ec9740f3
iuc
parents:
26
diff
changeset
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72 |
| 1 | 73 |
| 74 @REFERENCES@ | |
| 75 ]]> | |
| 76 </help> | |
| 77 <expand macro="citations" /> | |
| 78 </tool> |