Mercurial > repos > iuc > bedtools
annotate clusterBed.xml @ 12:7b3aaff0d78c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
| author | iuc |
|---|---|
| date | Fri, 28 Oct 2016 12:54:40 -0400 |
| parents | 7308cc546a36 |
| children | 95a3b2c25bd1 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bedtools_clusterbed" name="ClusterBed" version="@WRAPPER_VERSION@.0"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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1
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changeset
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2 <description>cluster overlapping/nearby intervals</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 1 | 9 <![CDATA[ |
| 0 | 10 bedtools cluster |
| 11 $strand | |
| 12 -d $distance | |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
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13 -i '$inputA' |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
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14 > '$output' |
| 1 | 15 ]]> |
| 0 | 16 </command> |
| 17 <inputs> | |
| 18 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
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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 | 20 help="That is, only cluster features that are the same strand. By default, this is disabled." /> |
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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 | 23 help="Default is 0. That is, overlapping and/or book-ended features are clustered." /> |
| 24 </inputs> | |
| 25 <outputs> | |
| 1 | 26 <data format_source="inputA" name="output" metadata_source="inputA"/> |
| 0 | 27 </outputs> |
| 1 | 28 <tests> |
| 29 <test> | |
| 30 <param name="inputA" value="mergedBed1.bed" ftype="bed" /> | |
| 31 <output name="output" file="clusterBed_result.bed" ftype="bed" /> | |
| 32 </test> | |
| 33 </tests> | |
| 0 | 34 <help> |
| 1 | 35 <![CDATA[ |
| 0 | 36 **What it does** |
| 37 | |
| 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. | |
| 39 | |
| 40 .. image:: $PATH_TO_IMAGES/cluster-glyph.png | |
| 41 | |
| 42 .. class:: warningmark | |
| 43 | |
| 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). | |
| 45 | |
| 46 @REFERENCES@ | |
| 1 | 47 ]]> |
| 0 | 48 </help> |
| 49 <expand macro="citations" /> | |
| 50 </tool> |