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1 <tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.1">
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2 <requirements>
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3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
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4 <!-- <requirement type="package" version="0.1.18">samtools</requirement> -->
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5 </requirements>
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6 <description>Intersect VCF and BED datasets</description>
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7 <command>
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8 #if str($bed_vs_interval.bed_vs_interval_selector) == "bed":
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9 vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}"
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10 #else:
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11 vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}"
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12 #end if
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13
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14 </command>
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15 <inputs>
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16 <!-- selecting refernce source -->
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17 <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" />
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18 <conditional name="bed_vs_interval">
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19 <param name="bed_vs_interval_selector" type="select" label="Intersect with BED dataset or an interval">
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20 <option value="bed">BED</option>
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21 <option value="interval">Interval</option>
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22 </param>
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23 <when value="bed">
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24 <param name="bed_input" type="data" format="bed" label="Select BED dataset" />
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25 </when>
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26 <when value="interval">
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27 <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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28 </when>
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29 </conditional>
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30 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." />
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31 </inputs>
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32 <outputs>
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33 <data format="vcf" name="out_file1" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="bed_vs_interval_selector" value="bed" />
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38 <param name="bed_input" value="vcfannotate.bed" />
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39 <param name="invert" value="False" />
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40 <param name="vcf_input" value="vcflib.vcf"/>
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41 <output name="out_file1" file="vcfbedintersect-test1.vcf"/>
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42 </test>
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43 <test>
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44 <param name="bed_vs_interval_selector" value="interval" />
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45 <param name="int_input" value="20:1-30000" />
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46 <param name="invert" value="False" />
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47 <param name="vcf_input" value="vcflib.vcf"/>
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48 <output name="out_file1" file="vcfbedintersect-test2.vcf"/>
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49 </test>
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50 </tests>
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51
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52 <help>
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53
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54 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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55
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56 ----
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57
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58 VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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59
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60 </help>
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61 </tool>
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