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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 08:05:00 -0500
parents 9edfe5145ba8
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9edfe5145ba8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
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1 <tool id="vcfbedintersect" name="VCF-BEDintersect:" version="@WRAPPER_VERSION@+galaxy0">
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31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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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>
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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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 #if str($bed_vs_interval.bed_vs_interval_selector) == "bed":
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aea8e90ad788 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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10 vcfintersect -b '${bed_vs_interval.bed_input}' ${invert} '${vcf_input}' > '${out_file1}'
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31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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11 #else:
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aea8e90ad788 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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12 vcfintersect -R '${bed_vs_interval.int_input}' ${invert} '${vcf_input}' > '${out_file1}'
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31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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13 #end if
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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14 </command>
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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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" />
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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18 <conditional name="bed_vs_interval">
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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19 <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with">
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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20 <option value="bed">BED</option>
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 <option value="interval">Interval</option>
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22 </param>
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23 <when value="bed">
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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24 <param name="bed_input" type="data" format="bed" label="Select BED dataset" />
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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25 </when>
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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26 <when value="interval">
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27 <param name="int_input" type="text" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" />
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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28 </when>
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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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." />
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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31 </inputs>
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32 <outputs>
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33 <data format="vcf" name="out_file1" />
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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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" />
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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38 <param name="bed_input" value="vcfannotate.bed" ftype="bed" />
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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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 <help>
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52 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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53
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54 ----
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55
31a86dbe17c0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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56 VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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57 </help>
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58 <expand macro="citations" />
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59 </tool>