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1 <tool id="vcftools_merge" name="Merge" version="0.1">
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2 <description>multiple VCF datasets</description>
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3
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4 <requirements>
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5 <requirement type="package">tabix</requirement>
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6 <requirement type="package" version="0.1.11">vcftools</requirement>
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7 </requirements>
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8
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9 <command>
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10 ## Preprocessing for each dataset.
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11 #set dataset_names = []
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12 #for i, $input in enumerate( $inputs ):
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13 ## Sort file.
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14 vcf-sort ${input.file} > ${i}.vcf.sorted ;
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15
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16 ## Compress.
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17 bgzip ${i}.vcf.sorted ;
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18
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19 ## Index.
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20 tabix -p vcf ${i}.vcf.sorted.gz ;
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21
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22 #silent dataset_names.append( str($i) + '.vcf.sorted.gz' )
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23 #end for
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24
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25 ## Merge.
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26 vcf-merge
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27 #echo ' '.join( dataset_names ) # > ${output}
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28
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29 </command>
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30 <inputs>
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31 <repeat name="inputs" title="Datasets to Merge" min="2">
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32 <param name="file" label="Dataset" type="data" format="vcf"/>
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33 </repeat>
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34 </inputs>
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35
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36 <outputs>
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37 <data name="output" format="vcf"/>
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38 </outputs>
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39
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40 <stdio>
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41 <regex match=".*" source="both" level="log" description="tool progress"/>
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42 </stdio>
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43
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44 <tests>
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45 <!-- Cannot specify multiple repeats in test framework right now, so no tests possible. -->
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46 </tests>
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47
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48 <help>
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49 Please see the VCFtools `documentation`__ for help and further information.
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50
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51 .. __: http://vcftools.sourceforge.net/docs.html
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52 </help>
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53 </tool>
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