bedtools: mapBed.xml annotate

annotate mapBed.xml @ 55:678ea22d643d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"

author	iuc
date	Thu, 06 May 2021 14:14:33 +0000
parents	b06c53665eb6
children	7a06bb42dbb1

rev	line source
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	1 <tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2">
17 a2d4c30ba2f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 16 diff changeset	2 <description>apply a function to a column for each overlapping interval</description>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	3 <macros>
0d3aa592ce27 Uploaded iuc parents: diff changeset	4 <import>macros.xml</import>
0d3aa592ce27 Uploaded iuc parents: diff changeset	5 </macros>
0d3aa592ce27 Uploaded iuc parents: diff changeset	6 <expand macro="requirements" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	7 <expand macro="stdio" />
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	8 <command><![CDATA[
47 33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	9 bedtools map
33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	10 -a '${inputA}'
33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	11 -b '${inputB}'
33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	12 $strand
33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	13 @C_AND_O_ARGUMENT@
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	14 @OVERLAP@
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	15 #if str($overlapB):
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	16 -F $overlapB
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	17 #end if
47 33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	18 $reciprocal
33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	19 $split
33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	20 $header
33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	21 @GENOME_FILE_MAPBED@
33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	22 > '${output}'
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	23 ]]></command>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	24 <inputs>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	25 <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	26 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	27 <expand macro="overlap" />
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	28 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	29 <param name="reciprocal" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	30 label="Require reciprocal overlap"
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	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" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	32 <expand macro="strand2" />
16 e30113df8cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 7b8a4ffc823f4dab194f1c629b7e83277dbe4337 iuc parents: 15 diff changeset	33 <expand macro="c_and_o_argument">
47 33c2e424ad7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184 iuc parents: 42 diff changeset	34 <param name="col" argument="-c" type="data_column" data_ref="inputB" label="Specify the column(s) from the B file to map onto intervals in A" help="Multiple columns can be specified in a comma-delimited list" />
16 e30113df8cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 7b8a4ffc823f4dab194f1c629b7e83277dbe4337 iuc parents: 15 diff changeset	35 </expand>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	36 <expand macro="split" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	37 <expand macro="print_header" />
54 b06c53665eb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22" iuc parents: 50 diff changeset	38 <expand macro="input_optional_genome_file" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	39 </inputs>
0d3aa592ce27 Uploaded iuc parents: diff changeset	40 <outputs>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	41 <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	42 </outputs>
0d3aa592ce27 Uploaded iuc parents: diff changeset	43 <tests>
0d3aa592ce27 Uploaded iuc parents: diff changeset	44 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	45 <param name="inputA" value="mapBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	46 <param name="inputB" value="mapBed2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	47 <repeat name="c_and_o_argument_repeat">
13 bdb4509d9482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e8e971905f5fce11a99d51b1399af45288389d76 iuc parents: 8 diff changeset	48 <param name="col" value="5" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	49 <param name="operation" value="mean" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	50 </repeat>
0d3aa592ce27 Uploaded iuc parents: diff changeset	51 <output name="output" file="mapBed_result1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	52 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	53 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	54 <param name="inputA" value="mapBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	55 <param name="inputB" value="mapBed2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	56 <repeat name="c_and_o_argument_repeat">
0d3aa592ce27 Uploaded iuc parents: diff changeset	57 <param name="col" value="5" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	58 <param name="operation" value="collapse" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	59 </repeat>
0d3aa592ce27 Uploaded iuc parents: diff changeset	60 <output name="output" file="mapBed_result2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	61 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	62 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	63 <param name="inputA" value="mapBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	64 <param name="inputB" value="mapBed2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	65 <repeat name="c_and_o_argument_repeat">
13 bdb4509d9482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e8e971905f5fce11a99d51b1399af45288389d76 iuc parents: 8 diff changeset	66 <param name="col" value="5" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	67 <param name="operation" value="collapse" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	68 </repeat>
0d3aa592ce27 Uploaded iuc parents: diff changeset	69 <param name="strand" value="-S" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	70 <output name="output" file="mapBed_result3.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	71 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	72 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	73 <param name="inputA" value="mapBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	74 <param name="inputB" value="mapBed2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	75 <repeat name="c_and_o_argument_repeat">
13 bdb4509d9482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e8e971905f5fce11a99d51b1399af45288389d76 iuc parents: 8 diff changeset	76 <param name="col" value="5" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	77 <param name="operation" value="collapse" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	78 </repeat>
0d3aa592ce27 Uploaded iuc parents: diff changeset	79 <param name="strand" value="-s" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	80 <output name="output" file="mapBed_result4.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	81 </test>
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	82 <test>
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	83 <param name="inputA" value="mapBed3.bed" ftype="bed" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	84 <param name="inputB" value="mapBed4.bed" ftype="bed" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	85 <repeat name="c_and_o_argument_repeat">
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	86 <param name="col" value="5" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	87 <param name="operation" value="collapse" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	88 </repeat>
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	89 <param name="strand" value="-s" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	90 <param name="genome_choose" value="-g" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	91 <param name="genome_file_opts_selector" value="hist" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	92 <param name="genome" value="mm9.len" ftype="bed" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	93 <output name="output" file="mapBed_result5.bed" ftype="bed" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	94 </test>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	95 </tests>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	96 <help><![CDATA[
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	97 What it does
0d3aa592ce27 Uploaded iuc parents: diff changeset	98
0d3aa592ce27 Uploaded iuc parents: diff changeset	99 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.
0d3aa592ce27 Uploaded iuc parents: diff changeset	100
0d3aa592ce27 Uploaded iuc parents: diff changeset	101 .. image:: $PATH_TO_IMAGES/map-glyph.png
0d3aa592ce27 Uploaded iuc parents: diff changeset	102
0d3aa592ce27 Uploaded iuc parents: diff changeset	103 .. class:: infomark
0d3aa592ce27 Uploaded iuc parents: diff changeset	104
0d3aa592ce27 Uploaded iuc parents: diff changeset	105 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.
0d3aa592ce27 Uploaded iuc parents: diff changeset	106
0d3aa592ce27 Uploaded iuc parents: diff changeset	107 .. class:: infomark
0d3aa592ce27 Uploaded iuc parents: diff changeset	108
0d3aa592ce27 Uploaded iuc parents: diff changeset	109 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.
0d3aa592ce27 Uploaded iuc parents: diff changeset	110
0d3aa592ce27 Uploaded iuc parents: diff changeset	111 @REFERENCES@
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	112 ]]></help>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	113 <expand macro="citations" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	114 </tool>

Mercurial > repos > iuc > bedtools

annotate mapBed.xml @ 55:678ea22d643d draft