bedtools: shuffleBed.xml annotate

annotate shuffleBed.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

author	iuc
date	Mon, 29 Apr 2019 05:55:48 -0400
parents	4f7a5ccd2ae9
children	ce3c7f062223

rev	line source
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	1 <tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@">
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>randomly redistrubute intervals in a genome</description>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	3 <macros>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	4 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	5 </macros>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	6 <expand macro="requirements" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	7 <expand macro="stdio" />
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	8 <command><![CDATA[
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	9 bedtools shuffle
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	10 -g @GENOME_FILE@
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	11 -i '$inputA'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	12 $bedpe
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	13 #if str($seed.seed_choose) == "True":
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	14 -seed $seed.seed
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	15 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	16 #if str($add_bed.add_bed_select) == "not_be":
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	17 -excl $add_bed.excl
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	18 #if str($add_bed.overlap)
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	19 -f $add_bed.overlap
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	20 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	21 #elif str($add_bed.add_bed_select) == "be":
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	22 -incl $add_bed.incl
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	23 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	24 $chrom
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	25 $chromfirst
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	26 $no_overlap
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	27 $allow_beyond
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	28 -maxTries $maxtries
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	29 > '$output'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	30 ]]></command>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	31 <inputs>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	32 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	33 <param argument="-bedpe" type="boolean" truevalue="-bedpe" falsevalue="" checked="false" label="The file is in BEDPE format" />
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	34 <expand macro="input_conditional_genome_file" />
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	35 <param argument="-chrom" type="boolean" truevalue="-chrom" falsevalue="" checked="false"
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	36 label="Keep features in the input file on the same chromosome"
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen." />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	38 <expand macro="seed" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	39 <conditional name="add_bed">
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	40 <param name="add_bed_select" type="select" label="Choose an additional BED file">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	41 <option value="no" selected="true">No additional BED file</option>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	42 <option value="not_be">Coordinates in which features from -i should not be placed?</option>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	43 <option value="be">coordinates in which features from -i should be placed?</option>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	44 </param>
3 2cd7e321d259 Uploaded iuc parents: 1 diff changeset	45 <when value="no" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	46 <when value="not_be">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	47 <param argument="-excl" type="data" format="bed" label="Choose File" />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	48 <expand macro="fraction" name="overlap" argument="-f" label="Maximum overlap (as a fraction of the -i feature) with an -excl feature that is tolerated before searching for a new, randomized locus" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	49 </when>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	50 <when value="be">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	51 <param argument="-incl" type="data" format="bed" label="Choose File" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	52 </when>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	53 </conditional>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	54 <param name="chromfirst" argument="-chromFirst" type="boolean" truevalue="-chromFirst" falsevalue="" checked="false"
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	55 label="Choose chromosome first"
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	56 help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size." />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	57 <param name="maxtries" argument="-maxTries" type="integer" value="1000"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	58 label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	59 <param name="no_overlap" argument="-noOverlapping" type="boolean" truevalue="-noOverlapping" falsevalue="" checked="false"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	60 label="Don’t allow shuffled intervals to overlap" />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	61 <param name="allow_beyond" argument="-allowBeyondChromEnd" type="boolean" truevalue="-allowBeyondChromEnd" falsevalue="" checked="false"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	63 </inputs>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	64 <outputs>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	65 <data name="output" format="bed" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	66 </outputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	67 <tests>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	68 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	69 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	70 <param name="genome_file_opts_selector" value="hist" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	71 <param name="genome" value="shuffleBed.len" ftype="tabular" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	72 <param name="chrom" value="" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	73 <param name="seed_choose" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	74 <param name="seed" value="1" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	75 <output name="output" file="shuffleBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	76 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	77 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	78 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	79 <param name="genome_file_opts_selector" value="hist" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	80 <param name="genome" value="shuffleBed.len" ftype="tabular" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	81 <param name="chrom" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	82 <param name="seed_choose" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	83 <param name="seed" value="1" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	84 <output name="output" file="shuffleBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	85 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	86 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	87 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	88 <param name="genome_file_opts_selector" value="hist" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	89 <param name="genome" value="shuffleBed.len" ftype="tabular" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	90 <param name="excl" value="shuffleBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	91 <param name="seed_choose" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	92 <param name="seed" value="1" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	93 <output name="output" file="shuffleBed_result3.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	94 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	95 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	96 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	97 <param name="genome_file_opts_selector" value="hist" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	98 <param name="genome" value="shuffleBed.len" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	99 <param name="allow_beyond" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	100 <param name="seed_choose" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	101 <param name="seed" value="1" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	102 <output name="output" file="shuffleBed_result4.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	103 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	104 </tests>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	105 <help><![CDATA[
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	106 What it does
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	107
26 95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 19 diff changeset	108 bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” @STD_BEDTOOLS_INPUT_LABEL@ file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the significance of associations of one feature with another.
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	109
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	110 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	111
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	112 @REFERENCES@
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	113 ]]></help>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	114 <expand macro="citations" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	115 </tool>

Mercurial > repos > iuc > bedtools

annotate shuffleBed.xml @ 34:dde39ba9c031 draft