Mercurial > repos > iuc > bedtools
annotate overlapBed.xml @ 48:2f457890d8c8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
| author | iuc |
|---|---|
| date | Tue, 11 Dec 2018 13:59:34 -0500 |
| parents | d279800f4ff9 |
| children | df28283b3778 |
| rev | line source |
|---|---|
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48
2f457890d8c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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42
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changeset
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1 <tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@WRAPPER_VERSION@"> |
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17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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8
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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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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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17
diff
changeset
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11 -i '$input' |
| 8 | 12 -cols $cols |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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13 > '$output' |
| 8 | 14 ]]> |
| 15 </command> | |
| 16 <inputs> | |
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42
d279800f4ff9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents:
26
diff
changeset
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17 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
| 8 | 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> |