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annotate vcfcombine.xml @ 0:a9ce47a1d653 draft

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author devteam
date Mon, 09 Nov 2015 12:30:48 -0500
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a9ce47a1d653 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="vcfcombine" name="VCFcombine:" version="0.0.4">
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2 <description>Combine multiple VCF 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
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10 vcfcombine
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11
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12 #for $input_vcf in $input_vcfs:
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13 "${input_vcf}"
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14 #end for
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16 > "${out_file1}"
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18 </command>
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19 <inputs>
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20 <param name="input_vcfs" type="data" format="vcf" label="Select VCF Datasets" min="2" multiple="True"/>
a9ce47a1d653 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 </inputs>
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22 <outputs>
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23 <data format="vcf" name="out_file1" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input_vcfs" value="vcflib.vcf"/>
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28 <output name="out_file1" file="vcfcombine-test1.vcf"/>
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29 </test>
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30 </tests>
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31 <help>
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32
a9ce47a1d653 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files, which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted.
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34
a9ce47a1d653 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 -----
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a9ce47a1d653 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 Vcfcombine @IS_PART_OF_VCFLIB@
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38 </help>
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39 <expand macro="citations" />
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40 </tool>