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1 <tool id="bedtools_subtractbed" name="SubtractBed" version="@WRAPPER_VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 bedtools subtract
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11 $strand
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12 -a $inputA
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13 -b $inputB
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14 -f $overlap
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15 $removeIfOverlap
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16 > $output
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
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21 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
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22 <expand macro="strand2" />
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23 <expand macro="overlap" />
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24 <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
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25 <option value="" selected="True">Dont Remove entire feature on overlap</option>
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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>
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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>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data format_source="inputA" name="output" metadata_source="inputA"/>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="inputA" value="subtractBed1.bed" ftype="bed" />
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36 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
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37 <output name="output" file="subtractBed_result1.bed" ftype="bed" />
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38 </test>
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39 <test>
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40 <param name="inputA" value="subtractBed1.bed" ftype="bed" />
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41 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
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42 <param name="overlap" value="0.80" />
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43 <output name="output" file="subtractBed_result2.bed" ftype="bed" />
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44 </test>
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45 <test>
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46 <param name="inputA" value="subtractBed1.bed" ftype="bed" />
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47 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
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48 <param name="removeIfOverlap" value="-A" />
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49 <output name="output" file="subtractBed_result3.bed" ftype="bed" />
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50 </test>
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51 </tests>
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52 <help>
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53 <![CDATA[
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54 **What it does**
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55
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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.
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57
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58 .. image:: $PATH_TO_IMAGES/subtract-glyph.png
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59
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60 @REFERENCES@
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61 ]]>
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62 </help>
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63 <expand macro="citations" />
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64 </tool>
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