Mercurial > repos > iuc > bedtools
annotate subtractBed.xml @ 17:a2d4c30ba2f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
| author | iuc |
|---|---|
| date | Sun, 21 Jun 2015 22:49:46 -0400 |
| parents | 0d3aa592ce27 |
| children | c0fbce5dc84a |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_subtractbed" name="SubtractBed" version="@WRAPPER_VERSION@.0"> |
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17
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>remove intervals based on overlaps</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 subtract | |
| 11 $strand | |
| 12 -a $inputA | |
| 13 -b $inputB | |
| 14 -f $overlap | |
| 15 $removeIfOverlap | |
| 16 > $output | |
| 17 ]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
| 21 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/> | |
| 22 <expand macro="strand2" /> | |
| 23 <expand macro="overlap" /> | |
| 24 <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?"> | |
| 25 <option value="" selected="True">Dont Remove entire feature on overlap</option> | |
| 26 <option value="-A">Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed</option> | |
| 27 <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature)</option> | |
| 28 </param> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data format_source="inputA" name="output" metadata_source="inputA"/> | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name="inputA" value="subtractBed1.bed" ftype="bed" /> | |
| 36 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> | |
| 37 <output name="output" file="subtractBed_result1.bed" ftype="bed" /> | |
| 38 </test> | |
| 39 <test> | |
| 40 <param name="inputA" value="subtractBed1.bed" ftype="bed" /> | |
| 41 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> | |
| 42 <param name="overlap" value="0.80" /> | |
| 43 <output name="output" file="subtractBed_result2.bed" ftype="bed" /> | |
| 44 </test> | |
| 45 <test> | |
| 46 <param name="inputA" value="subtractBed1.bed" ftype="bed" /> | |
| 47 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> | |
| 48 <param name="removeIfOverlap" value="-A" /> | |
| 49 <output name="output" file="subtractBed_result3.bed" ftype="bed" /> | |
| 50 </test> | |
| 51 </tests> | |
| 52 <help> | |
| 53 <![CDATA[ | |
| 54 **What it does** | |
| 55 | |
| 56 bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported. | |
| 57 | |
| 58 .. image:: $PATH_TO_IMAGES/subtract-glyph.png | |
| 59 | |
| 60 @REFERENCES@ | |
| 61 ]]> | |
| 62 </help> | |
| 63 <expand macro="citations" /> | |
| 64 </tool> |