annotate shuffleBed.xml @ 22:bd7721ad15aa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
author iuc
date Sun, 21 Jan 2018 07:17:19 -0500
parents a8eabd2838f6
children 95a3b2c25bd1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
a8eabd2838f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents: 17
diff changeset
1 <tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0">
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" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
8 <command>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
9 <![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
10 bedtools shuffle
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
11 -g @GENOME_FILE@
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 10
diff changeset
12 -i '$inputA'
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
13 $bedpe
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
14 #if str($seed.seed_choose) == "True":
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
15 -seed $seed.seed
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
16 #end if
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
17 #if str($add_bed.add_bed_select) == "not_be":
6
d25966c8ddeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f-dirty
iuc
parents: 4
diff changeset
18 -excl $add_bed.excl
d25966c8ddeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f-dirty
iuc
parents: 4
diff changeset
19 -f $add_bed.overlap
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
20 #elif str($add_bed.add_bed_select) == "be":
6
d25966c8ddeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f-dirty
iuc
parents: 4
diff changeset
21 -incl $add_bed.incl
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
22 #end if
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
23 $chrom
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
24 $chromfirst
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
25 $no_overlap
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
26 $allow_beyond
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
27 -maxTries $maxtries
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 10
diff changeset
28 > '$output'
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
29 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
30 </command>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
31 <inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
10
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 6
diff changeset
33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" />
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" />
10
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 6
diff changeset
35 <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue=""
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
36 label="Keep features in the input file on the same chromosome"
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" />
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">
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
41 <option value="no" selected="True">No additional BED file</option>
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">
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
47 <param name="excl" type="data" format="bed" label="Choose File" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
48 <expand macro="overlap" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
49 </when>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
50 <when value="be">
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
51 <param name="incl" type="data" format="bed" label="Choose File" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
52 </when>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
53 </conditional>
10
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 6
diff changeset
54 <param name="chromfirst" type="boolean" checked="False" truevalue="-chromFirst" falsevalue=""
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
55 label="Choose chromosome first"
82aac94b06c3 Uploaded
iuc
parents: 0
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. (-chromFirst)" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
57 <param name="maxtries" type="integer" value="1000"
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
58 label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" />
10
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 6
diff changeset
59 <param name="no_overlap" type="boolean" checked="False" truevalue="-noOverlapping" falsevalue=""
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
60 label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" />
10
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 6
diff changeset
61 <param name="allow_beyond" type="boolean" checked="False" truevalue="-allowBeyondChromEnd" falsevalue=""
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
63 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
64 <outputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
65 <data format="bed" name="output" />
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>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
105 <help>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
106 <![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
107 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
108
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
109 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” BED/GFF/VCF 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
110
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
111 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
112
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
113 @REFERENCES@
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
114 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
115 </help>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
116 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
117 </tool>