Mercurial > repos > iuc > bedtools

annotate sortBed.xml @ 39:3e38c9b3214f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
author iuc
date Wed, 01 Sep 2021 11:04:15 +0000
parents ce3c7f062223
children 7ab85ac5f64b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
39
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 37
diff changeset
1 <tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@" profile="@PROFILE@">
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
2 <description>order the intervals</description>
39
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 37
diff changeset
3 <expand macro="bio_tools" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
4 <macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
5 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
6 </macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
7 <expand macro="requirements" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
8 <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
9 <command><![CDATA[
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
10 sortBed
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
11 -i '$input'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
12 $option
37
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
13 @GENOME_FILE_MAPBED@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
14 > '$output'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
15 ]]></command>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
16 <inputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
17 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
18 <param name="option" type="select" label="Sort by">
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
19 <!-- sort -k 1,1 -k2,2 -n a.bed -->
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
20 <option value="">chromosome, then by start position (asc)</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
21 <option value="-sizeA">feature size in ascending order.</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
22 <option value="-sizeD">feature size in descending order.</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
23 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
24 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
27 </param>
37
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
28 <expand macro="input_optional_genome_file" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
29 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
30 <outputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
31 <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
32 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
33 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
34 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
35 <param name="input" value="sortBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
36 <param name="option" value="" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
37 <output name="output" file="sortBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
38 </test>
37
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
39 <test>
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
40 <param name="input" value="sortBed2.bed" ftype="bed" />
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
41 <param name="option" value="" />
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
42 <output name="output" file="sortBed_result2.bed" ftype="bed" />
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
43 </test>
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
44 <test>
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
45 <param name="input" value="sortBed2.bed" ftype="bed" />
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
46 <param name="option" value="" />
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
47 <param name="genome_choose" value="-g" />
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
48 <param name="genome_file_opts_selector" value="hist" />
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
49 <param name="genome" value="mm9.len" ftype="bed" />
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
50 <output name="output" file="sortBed_result3.bed" ftype="bed" />
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 34
diff changeset
51 </test>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
52 </tests>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
53 <help><![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
54 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
55
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
56 Sorts a feature file by chromosome and other criteria.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
57
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
58
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
59 .. class:: warningmark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
60
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
61 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
62 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
63 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
64
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
65 @REFERENCES@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
66 ]]></help>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
67 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
68 </tool>