bedtools: shuffleBed.xml annotate

annotate shuffleBed.xml @ 50:df28283b3778 draft

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

author	iuc
date	Mon, 29 Apr 2019 05:54:22 -0400
parents	2f457890d8c8
children	b06c53665eb6

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_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@">
17 a2d4c30ba2f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 13 diff changeset	2 <description>randomly redistrubute intervals in a genome</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[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	9 bedtools shuffle
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	10 -g @GENOME_FILE@
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	11 -i '$inputA'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	12 $bedpe
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	13 #if str($seed.seed_choose) == "True":
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	14 -seed $seed.seed
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	15 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	16 #if str($add_bed.add_bed_select) == "not_be":
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	17 -excl $add_bed.excl
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	18 #if str($add_bed.overlap)
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	19 -f $add_bed.overlap
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	20 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	21 #elif str($add_bed.add_bed_select) == "be":
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	22 -incl $add_bed.incl
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	23 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	24 $chrom
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	25 $chromfirst
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	26 $no_overlap
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	27 $allow_beyond
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	28 -maxTries $maxtries
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	29 > '$output'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	30 ]]></command>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	31 <inputs>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	32 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	33 <param argument="-bedpe" type="boolean" truevalue="-bedpe" falsevalue="" checked="false" label="The file is in BEDPE format" />
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	34 <expand macro="input_conditional_genome_file" />
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	35 <param argument="-chrom" type="boolean" truevalue="-chrom" falsevalue="" checked="false"
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	36 label="Keep features in the input file on the same chromosome"
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen." />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	38 <expand macro="seed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	39 <conditional name="add_bed">
0d3aa592ce27 Uploaded iuc parents: diff changeset	40 <param name="add_bed_select" type="select" label="Choose an additional BED file">
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	41 <option value="no" selected="true">No additional BED file</option>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	42 <option value="not_be">Coordinates in which features from -i should not be placed?</option>
0d3aa592ce27 Uploaded iuc parents: diff changeset	43 <option value="be">coordinates in which features from -i should be placed?</option>
0d3aa592ce27 Uploaded iuc parents: diff changeset	44 </param>
13 bdb4509d9482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e8e971905f5fce11a99d51b1399af45288389d76 iuc parents: 8 diff changeset	45 <when value="no" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	46 <when value="not_be">
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	47 <param argument="-excl" type="data" format="bed" label="Choose File" />
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 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" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	49 </when>
0d3aa592ce27 Uploaded iuc parents: diff changeset	50 <when value="be">
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	51 <param argument="-incl" type="data" format="bed" label="Choose File" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	52 </when>
0d3aa592ce27 Uploaded iuc parents: diff changeset	53 </conditional>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	54 <param name="chromfirst" argument="-chromFirst" type="boolean" truevalue="-chromFirst" falsevalue="" checked="false"
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	55 label="Choose chromosome first"
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 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." />
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	57 <param name="maxtries" argument="-maxTries" type="integer" value="1000"
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	58 label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" />
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	59 <param name="no_overlap" argument="-noOverlapping" type="boolean" truevalue="-noOverlapping" falsevalue="" checked="false"
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	60 label="Don’t allow shuffled intervals to overlap" />
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	61 <param name="allow_beyond" argument="-allowBeyondChromEnd" type="boolean" truevalue="-allowBeyondChromEnd" falsevalue="" checked="false"
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	63 </inputs>
0d3aa592ce27 Uploaded iuc parents: diff changeset	64 <outputs>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	65 <data name="output" format="bed" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	66 </outputs>
0d3aa592ce27 Uploaded iuc parents: diff changeset	67 <tests>
0d3aa592ce27 Uploaded iuc parents: diff changeset	68 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	69 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	70 <param name="genome_file_opts_selector" value="hist" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	71 <param name="genome" value="shuffleBed.len" ftype="tabular" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	72 <param name="chrom" value="" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	73 <param name="seed_choose" value="True" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	74 <param name="seed" value="1" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	75 <output name="output" file="shuffleBed_result1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	76 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	77 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	78 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	79 <param name="genome_file_opts_selector" value="hist" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	80 <param name="genome" value="shuffleBed.len" ftype="tabular" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	81 <param name="chrom" value="True" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	82 <param name="seed_choose" value="True" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	83 <param name="seed" value="1" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	84 <output name="output" file="shuffleBed_result2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	85 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	86 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	87 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	88 <param name="genome_file_opts_selector" value="hist" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	89 <param name="genome" value="shuffleBed.len" ftype="tabular" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	90 <param name="excl" value="shuffleBed2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	91 <param name="seed_choose" value="True" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	92 <param name="seed" value="1" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	93 <output name="output" file="shuffleBed_result3.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	94 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	95 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	96 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	97 <param name="genome_file_opts_selector" value="hist" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	98 <param name="genome" value="shuffleBed.len" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	99 <param name="allow_beyond" value="True" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	100 <param name="seed_choose" value="True" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	101 <param name="seed" value="1" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	102 <output name="output" file="shuffleBed_result4.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	103 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	104 </tests>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	105 <help><![CDATA[
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	106 What it does
0d3aa592ce27 Uploaded iuc parents: diff changeset	107
42 d279800f4ff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 35 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.
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	109
0d3aa592ce27 Uploaded iuc parents: diff changeset	110 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png
0d3aa592ce27 Uploaded iuc parents: diff changeset	111
0d3aa592ce27 Uploaded iuc parents: diff changeset	112 @REFERENCES@
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	113 ]]></help>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	114 <expand macro="citations" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	115 </tool>

Mercurial > repos > iuc > bedtools

annotate shuffleBed.xml @ 50:df28283b3778 draft