Mercurial > repos > iuc > bedtools
annotate overlapBed.xml @ 26:c0fbce5dc84a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
| author | iuc |
|---|---|
| date | Mon, 17 Oct 2016 10:13:20 -0400 |
| parents | a2d4c30ba2f9 |
| children | d279800f4ff9 |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_overlapbed" name="OverlapBed" version="@WRAPPER_VERSION@.0"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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2 <description>computes the amount of overlap from two intervals</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools overlap | |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
11 -i '$input' |
| 8 | 12 -cols $cols |
|
26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
13 > '$output' |
| 8 | 14 ]]> |
| 15 </command> | |
| 16 <inputs> | |
| 17 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> | |
| 18 <param name="cols" type="data_column" multiple="True" data_ref="input" | |
| 19 label="Specify the columns for the starts and ends of the features for which you’d like to compute the overlap/distance" | |
| 20 help="The columns must be listed in the following order: start1,end1,start2,end2" /> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data format_source="input" name="output" metadata_source="input" label="Overlap of ${input.name}"/> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="input" value="windowBed_result1.bed" ftype="bed" /> | |
| 28 <param name="cols" value="2,3,5,6" /> | |
| 29 <output name="output" file="overlapBed_result1.bed" ftype="bed" /> | |
| 30 </test> | |
| 31 </tests> | |
| 32 <help> | |
| 33 <![CDATA[ | |
| 34 **What it does** | |
| 35 | |
| 36 overlap computes the amount of overlap (in the case of positive values) or distance (in the case of negative values) between feature coordinates occurring on the same input line and reports the result at the end of the same line. In this way, it is a useful method for computing custom overlap scores from the output of other BEDTools. | |
| 37 | |
| 38 @REFERENCES@ | |
| 39 ]]> | |
| 40 </help> | |
| 41 <expand macro="citations" /> | |
| 42 </tool> |