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1 <tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.3">
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2 <description>Intersect VCF and BED datasets</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"></expand>
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7 <expand macro="stdio" />
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8 <command>
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9 #if str($bed_vs_interval.bed_vs_interval_selector) == "bed":
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10 vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}"
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11 #else:
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12 vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}"
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13 #end if
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14
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15 </command>
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16 <inputs>
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17 <!-- selecting refernce source -->
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18 <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" />
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19 <conditional name="bed_vs_interval">
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20 <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with">
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21 <option value="bed">BED</option>
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22 <option value="interval">Interval</option>
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23 </param>
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24 <when value="bed">
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25 <param name="bed_input" type="data" format="bed" label="Select BED dataset" />
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26 </when>
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27 <when value="interval">
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28 <param name="int_input" type="text" size="20" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" />
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29 </when>
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30 </conditional>
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31 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." />
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32 </inputs>
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33 <outputs>
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34 <data format="vcf" name="out_file1" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="bed_vs_interval_selector" value="bed" />
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39 <param name="bed_input" value="vcfannotate.bed" />
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40 <param name="invert" value="False" />
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41 <param name="vcf_input" value="vcflib.vcf"/>
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42 <output name="out_file1" file="vcfbedintersect-test1.vcf"/>
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43 </test>
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44 <test>
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45 <param name="bed_vs_interval_selector" value="interval" />
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46 <param name="int_input" value="20:1-30000" />
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47 <param name="invert" value="False" />
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48 <param name="vcf_input" value="vcflib.vcf"/>
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49 <output name="out_file1" file="vcfbedintersect-test2.vcf"/>
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50 </test>
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51 </tests>
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52
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53 <help>
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54
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55 Computes intersection between a VCF dataset and a set of genomic intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) or a manually typed interval (in the form of chr:start-end).
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56
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57 ----
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58
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59 VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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60 </help>
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61 <expand macro="citations" />
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62 </tool>
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