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comparison subtractBed.xml @ 4:315929597efb draft

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author iuc
date Wed, 07 Jan 2015 12:45:05 -0500
parents 7511823bdea1
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3:190a747ddaa8 4:315929597efb
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[
9 bedtools subtract 10 bedtools subtract
10 $strand 11 $strand
11 -a $inputA 12 -a $inputA
12 -b $inputB 13 -b $inputB
13 -f $overlap 14 -f $overlap
14 $removeIfOverlap 15 $removeIfOverlap
15 &gt; $output 16 > $output
17 ]]>
16 </command> 18 </command>
17 <inputs> 19 <inputs>
18 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> 20 <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"/> 21 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
20 <expand macro="strand2" /> 22 <expand macro="strand2" />
21 <expand macro="overlap" /> 23 <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?"> 24 <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
30 <option value="" selected="True">Dont Remove entire feature on overlap</option> 25 <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> 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>
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> 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>
33 </param> 28 </param>
34 </inputs> 29 </inputs>
35 <outputs> 30 <outputs>
36 <data format_source="inputA" name="output" metadata_source="inputA" label=""/> 31 <data format_source="inputA" name="output" metadata_source="inputA"/>
37 </outputs> 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>
38 <help> 52 <help>
39 53 <![CDATA[
40 **What it does** 54 **What it does**
41 55
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. 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.
43 57
44 .. image:: $PATH_TO_IMAGES/subtract-glyph.png 58 .. image:: $PATH_TO_IMAGES/subtract-glyph.png
45 59
46 @REFERENCES@ 60 @REFERENCES@
61 ]]>
47 </help> 62 </help>
48 <expand macro="citations" /> 63 <expand macro="citations" />
49 </tool> 64 </tool>