Mercurial > repos > iuc > bedtools

annotate clusterBed.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_clusterbed" name="bedtools ClusterBed" 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>cluster overlapping/nearby 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[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
10 bedtools cluster
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
11 $strand
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
12 -d $distance
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
13 -i '$inputA'
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
14 > '$output'
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
15 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
16 </command>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
17 <inputs>
26
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents: 11
diff changeset
18 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
19 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness."
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
20 help="That is, only cluster features that are the same strand. By default, this is disabled." />
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
21 <param name="distance" type="integer" value="0"
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
22 label="Maximum distance between features allowed for features to be clustered"
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
23 help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
24 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
25 <outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
26 <data format_source="inputA" name="output" metadata_source="inputA"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
27 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
28 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
29 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
30 <param name="inputA" value="mergedBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
31 <output name="output" file="clusterBed_result.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
32 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
33 </tests>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
34 <help>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
35 <![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
36 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
37
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
38 Similar to merge, cluster report each set of overlapping or “book-ended” features in an interval file. In contrast to merge, cluster does not flatten the cluster of intervals into a new meta-interval; instead, it assigns an unique cluster ID to each record in each cluster. This is useful for having fine control over how sets of overlapping intervals in a single interval file are combined.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
39
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
40 .. image:: $PATH_TO_IMAGES/cluster-glyph.png
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
41
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
42 .. class:: warningmark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
43
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
44 bedtools cluster requires that you presort your data by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files).
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
45
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
46 @REFERENCES@
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
47 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
48 </help>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
49 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
50 </tool>