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annotate vcfannotate.xml @ 0:90b4338559cd draft

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author devteam
date Mon, 09 Nov 2015 12:29:23 -0500
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90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="vcfannotate" name="VCFannotate:" version="0.0.3">
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2 <description>Intersect VCF records with BED annotations</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>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command>
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9 <inputs>
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10 <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/>
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12 <param name="key_option" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/>
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 </inputs>
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14 <outputs>
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15 <data format="vcf" name="out_file1" />
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="bed_data" value="vcfannotate.bed" ftype="bed"/>
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 <param name="key_option" value="BED-features"/>
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 <param name="input" value="vcflib.vcf"/>
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22 <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" />
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23 </test>
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24 </tests>
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25 <help>
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26
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file.
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28
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 -----
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31 .. class:: infomark
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32
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33
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34 **Example**:
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35
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 The following VCF line::
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37
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
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39 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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40
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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41 will appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen::
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42
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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43 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
90b4338559cd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
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45
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46 ----
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47
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48 Vcfannotate @IS_PART_OF_VCFLIB@
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49 </help>
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50 <expand macro="citations" />
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51 </tool>