Mercurial > repos > iuc > bedtools

annotate clusterBed.xml @ 61:9f6bd4c9479f 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 db0b91a784ca0c216345bc488d7d488babf1b53f"
author iuc
date Fri, 01 Apr 2022 19:00:48 +0000
parents 539958feb49c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
57
1d0a0d6a78b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 56
diff changeset
1 <tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@TOOL_VERSION@" profile="@PROFILE@">
17
a2d4c30ba2f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 8
diff changeset
2 <description>cluster overlapping/nearby intervals</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>
59
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
6 <expand macro="bio_tools" />
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
7 <expand macro="requirements" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
8 <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
9 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
10 bedtools cluster
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
11 $strand
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
12 -d $distance
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
13 -i '$inputA'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
14 > '$output'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
15 ]]></command>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
16 <inputs>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
17 <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
18 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness."
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
19 help="That is, only cluster features that are the same strand. By default, this is disabled." />
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
20 <param name="distance" argument="-d" type="integer" value="0"
26
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
21 label="Maximum distance between features allowed for features to be clustered"
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
22 help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
23 </inputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
24 <outputs>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
25 <data name="output" format_source="inputA" metadata_source="inputA"/>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
26 </outputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
27 <tests>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
28 <test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
29 <param name="inputA" value="mergedBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
30 <output name="output" file="clusterBed_result.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
31 </test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
32 </tests>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
33 <help><![CDATA[
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
34 **What it does**
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
35
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
36 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.
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
37
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
38 .. image:: $PATH_TO_IMAGES/cluster-glyph.png
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
39
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
40 .. class:: warningmark
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
41
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
42 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).
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
43
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
44 @REFERENCES@
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
45 ]]></help>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
46 <expand macro="citations" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
47 </tool>