Mercurial > repos > iuc > bedtools

annotate sortBed.xml @ 32:4f7a5ccd2ae9 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 fc3616bd1463afef9681cd7c431ac29f79e37e74
author iuc
date Tue, 11 Dec 2018 14:01:26 -0500
parents 95a3b2c25bd1
children dde39ba9c031
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 26
diff changeset
1 <tool id="bedtools_sortbed" name="bedtools SortBED" version="@WRAPPER_VERSION@">
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>
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[
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
10 sortBed
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
11 -i '$input'
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
12 $option
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
13 > '$output'
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
14 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
15 </command>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
16 <inputs>
26
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents: 11
diff changeset
17 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" 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>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
28 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
29 <outputs>
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
30 <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
31 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
32 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
33 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
34 <param name="input" value="sortBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
35 <param name="option" value="" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
36 <output name="output" file="sortBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
37 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
38 </tests>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
39 <help>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
40 <![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
41 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
42
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
43 Sorts a feature file by chromosome and other criteria.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
44
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
45
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
46 .. class:: warningmark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
47
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
48 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
49 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
50 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
51
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
52 @REFERENCES@
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
53 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
54 </help>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
55 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
56 </tool>