Mercurial > repos > iuc > bedtools
comparison subtractBed.xml @ 0:4fb5ea02b441 draft
Uploaded
| author | iuc |
|---|---|
| date | Tue, 15 Jul 2014 14:42:23 -0400 |
| parents | |
| children | 7511823bdea1 |
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| -1:000000000000 | 0:4fb5ea02b441 |
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| 1 <tool id="bedtools_subtractbed" name="SubtractBed" version="@WRAPPER_VERSION@.0"> | |
| 2 <description></description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 bedtools subtract | |
| 10 $strand | |
| 11 -a $inputA | |
| 12 -b $inputB | |
| 13 -f $overlap | |
| 14 $removeIfOverlap | |
| 15 > $output | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
| 19 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/> | |
| 20 <expand macro="strand2" /> | |
| 21 <expand macro="overlap" /> | |
| 22 | |
| 23 <param name="strand" type="select" label="Calculation based on strandedness?"> | |
| 24 <option value="" selected="True">Overlaps on either strand</option> | |
| 25 <option value="-s">Only overlaps occurring on the **same** strand.</option> | |
| 26 <option value="-S">Only overlaps occurring on the **opposite** strand.</option> | |
| 27 </param> | |
| 28 | |
| 29 <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?"> | |
| 30 <option value="" selected="True">Dont Remove entire feature on overlap</option> | |
| 31 <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> | |
| 32 <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature).</option> | |
| 33 </param> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data format_source="inputA" name="output" metadata_source="inputA" label=""/> | |
| 37 </outputs> | |
| 38 <help> | |
| 39 | |
| 40 **What it does** | |
| 41 | |
| 42 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. | |
| 43 | |
| 44 .. image:: $PATH_TO_IMAGES/subtract-glyph.png | |
| 45 | |
| 46 @REFERENCES@ | |
| 47 </help> | |
| 48 </tool> |