Mercurial > repos > iuc > bedtools
annotate mapBed.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 |
|---|---|
|
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
1 <tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0"> |
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4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
3
diff
changeset
|
2 <description>apply a function to a column for each overlapping interval</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 map |
| 1 | 11 -a "${inputA}" |
| 12 -b "${inputB}" | |
| 0 | 13 $strand |
| 2 | 14 @C_AND_O_ARGUMENT@ |
| 0 | 15 -f $overlap |
| 16 $reciprocal | |
| 17 $split | |
| 18 $header | |
| 19 #if $genome.genome_choose == "-g" : | |
| 20 -g $genome.genome | |
| 1 | 21 #end if |
| 22 > "${output}" | |
| 23 ]]> | |
| 0 | 24 </command> |
| 25 <inputs> | |
| 1 | 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)" /> | |
| 0 | 28 <expand macro="overlap" /> |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
29 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" |
| 1 | 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)" /> | |
| 0 | 32 <expand macro="strand2" /> |
| 3 | 33 <expand macro="c_and_o_argument"> |
| 34 <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" /> | |
| 35 </expand> | |
| 1 | 36 <expand macro="split" /> |
| 37 <expand macro="print_header" /> | |
| 0 | 38 <conditional name="genome"> |
| 1 | 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)" /> | |
| 0 | 41 <when value="-g"> |
| 42 <expand macro="genome" /> | |
| 43 </when> | |
|
4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
3
diff
changeset
|
44 <when value="" /> |
| 0 | 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> | |
| 1 | 50 <tests> |
| 51 <test> | |
| 52 <param name="inputA" value="mapBed1.bed" ftype="bed" /> | |
| 53 <param name="inputB" value="mapBed2.bed" ftype="bed" /> | |
| 2 | 54 <repeat name="c_and_o_argument_repeat"> |
| 3 | 55 <param name="col" value="5" /> |
| 2 | 56 <param name="operation" value="mean" /> |
| 57 </repeat> | |
| 1 | 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" /> | |
| 2 | 63 <repeat name="c_and_o_argument_repeat"> |
| 64 <param name="col" value="5" /> | |
| 65 <param name="operation" value="collapse" /> | |
| 66 </repeat> | |
| 1 | 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" /> | |
| 2 | 72 <repeat name="c_and_o_argument_repeat"> |
| 3 | 73 <param name="col" value="5" /> |
| 2 | 74 <param name="operation" value="collapse" /> |
| 75 </repeat> | |
| 1 | 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" /> | |
| 2 | 82 <repeat name="c_and_o_argument_repeat"> |
| 3 | 83 <param name="col" value="5" /> |
| 2 | 84 <param name="operation" value="collapse" /> |
| 85 </repeat> | |
| 1 | 86 <param name="strand" value="-s" /> |
| 87 <output name="output" file="mapBed_result4.bed" ftype="bed" /> | |
| 88 </test> | |
| 89 </tests> | |
| 0 | 90 <help> |
| 1 | 91 <![CDATA[ |
| 0 | 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@ | |
| 1 | 107 ]]> |
| 0 | 108 </help> |
| 109 <expand macro="citations" /> | |
| 110 </tool> |