Mercurial > repos > iuc > bedtools
annotate mapBed.xml @ 24:679fbed9d08f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9555dac6cbff70048b682a6514c7fbb2b7fbb975
| author | iuc |
|---|---|
| date | Mon, 05 Sep 2016 15:27:44 -0400 |
| parents | 102424c60727 |
| children | c0fbce5dc84a |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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2 <description>apply a function to a column for each overlapping interval</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 map | |
| 11 -a "${inputA}" | |
| 12 -b "${inputB}" | |
| 13 $strand | |
| 14 @C_AND_O_ARGUMENT@ | |
| 15 -f $overlap | |
| 16 $reciprocal | |
| 17 $split | |
| 18 $header | |
| 19 #if $genome.genome_choose == "-g" : | |
| 20 -g $genome.genome | |
| 21 #end if | |
| 22 > "${output}" | |
| 23 ]]> | |
| 24 </command> | |
| 25 <inputs> | |
| 26 <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" /> | |
| 27 <param format="bam,bed,gff,vcf,gff3" name="inputB" type="data" label="File B (BAM/BED/VCF/GFF)" /> | |
| 28 <expand macro="overlap" /> | |
| 29 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" | |
| 30 label="Require reciprocal overlap" | |
| 31 help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" /> | |
| 32 <expand macro="strand2" /> | |
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e30113df8cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 7b8a4ffc823f4dab194f1c629b7e83277dbe4337
iuc
parents:
15
diff
changeset
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33 <expand macro="c_and_o_argument"> |
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e30113df8cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 7b8a4ffc823f4dab194f1c629b7e83277dbe4337
iuc
parents:
15
diff
changeset
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34 <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" /> |
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e30113df8cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 7b8a4ffc823f4dab194f1c629b7e83277dbe4337
iuc
parents:
15
diff
changeset
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35 </expand> |
| 8 | 36 <expand macro="split" /> |
| 37 <expand macro="print_header" /> | |
| 38 <conditional name="genome"> | |
| 39 <param name="genome_choose" type="boolean" checked="false" truevalue="-g" falsevalue="" | |
| 40 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="(-g)" /> | |
| 41 <when value="-g"> | |
| 42 <expand macro="genome" /> | |
| 43 </when> | |
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102424c60727
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1cfbe7505ebac3b447c6ae0f0d76b42656496588
iuc
parents:
17
diff
changeset
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44 <when value="" /> |
| 8 | 45 </conditional> |
| 46 </inputs> | |
| 47 <outputs> | |
| 48 <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}"/> | |
| 49 </outputs> | |
| 50 <tests> | |
| 51 <test> | |
| 52 <param name="inputA" value="mapBed1.bed" ftype="bed" /> | |
| 53 <param name="inputB" value="mapBed2.bed" ftype="bed" /> | |
| 54 <repeat name="c_and_o_argument_repeat"> | |
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bdb4509d9482
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e8e971905f5fce11a99d51b1399af45288389d76
iuc
parents:
8
diff
changeset
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55 <param name="col" value="5" /> |
| 8 | 56 <param name="operation" value="mean" /> |
| 57 </repeat> | |
| 58 <output name="output" file="mapBed_result1.bed" ftype="bed" /> | |
| 59 </test> | |
| 60 <test> | |
| 61 <param name="inputA" value="mapBed1.bed" ftype="bed" /> | |
| 62 <param name="inputB" value="mapBed2.bed" ftype="bed" /> | |
| 63 <repeat name="c_and_o_argument_repeat"> | |
| 64 <param name="col" value="5" /> | |
| 65 <param name="operation" value="collapse" /> | |
| 66 </repeat> | |
| 67 <output name="output" file="mapBed_result2.bed" ftype="bed" /> | |
| 68 </test> | |
| 69 <test> | |
| 70 <param name="inputA" value="mapBed1.bed" ftype="bed" /> | |
| 71 <param name="inputB" value="mapBed2.bed" ftype="bed" /> | |
| 72 <repeat name="c_and_o_argument_repeat"> | |
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13
bdb4509d9482
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e8e971905f5fce11a99d51b1399af45288389d76
iuc
parents:
8
diff
changeset
|
73 <param name="col" value="5" /> |
| 8 | 74 <param name="operation" value="collapse" /> |
| 75 </repeat> | |
| 76 <param name="strand" value="-S" /> | |
| 77 <output name="output" file="mapBed_result3.bed" ftype="bed" /> | |
| 78 </test> | |
| 79 <test> | |
| 80 <param name="inputA" value="mapBed1.bed" ftype="bed" /> | |
| 81 <param name="inputB" value="mapBed2.bed" ftype="bed" /> | |
| 82 <repeat name="c_and_o_argument_repeat"> | |
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13
bdb4509d9482
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e8e971905f5fce11a99d51b1399af45288389d76
iuc
parents:
8
diff
changeset
|
83 <param name="col" value="5" /> |
| 8 | 84 <param name="operation" value="collapse" /> |
| 85 </repeat> | |
| 86 <param name="strand" value="-s" /> | |
| 87 <output name="output" file="mapBed_result4.bed" ftype="bed" /> | |
| 88 </test> | |
| 89 </tests> | |
| 90 <help> | |
| 91 <![CDATA[ | |
| 92 **What it does** | |
| 93 | |
| 94 bedtools map allows one to map overlapping features in a B file onto features in an A file and apply statistics and/or summary operations on those features. | |
| 95 | |
| 96 .. image:: $PATH_TO_IMAGES/map-glyph.png | |
| 97 | |
| 98 .. class:: infomark | |
| 99 | |
| 100 bedtools map requires each input file to be sorted by genome coordinate. For BED files, this can be done with sort -k1,1 -k2,2n. Other sorting criteria are allowed if a genome file (-g) is provides that specifies the expected chromosome order. | |
| 101 | |
| 102 .. class:: infomark | |
| 103 | |
| 104 The map tool is substantially faster in versions 2.19.0 and later. The plot below demonstrates the increased speed when, for example, counting the number of exome alignments that align to each exon. The bedtools times are compared to the bedops bedmap utility as a point of reference. | |
| 105 | |
| 106 @REFERENCES@ | |
| 107 ]]> | |
| 108 </help> | |
| 109 <expand macro="citations" /> | |
| 110 </tool> |