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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:35:52 -0500
parents eb02907453b4
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60743b92cc26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="vcftools_merge" name="Merge" version="0.1.1">
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2 <description>multiple VCF datasets</description>
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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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60743b92cc26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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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60743b92cc26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 #for $i, $input in enumerate( $input_files ):
60743b92cc26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 ## Sort file.
60743b92cc26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 vcf-sort ${input} > ${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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60743b92cc26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28
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29 </command>
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30 <inputs>
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60743b92cc26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 <param name="input_files" label="Datasets to Merge" type="data" format="vcf" min="2" multiple="True"/>
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32 </inputs>
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33
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34 <outputs>
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35 <data name="output" format="vcf"/>
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36 </outputs>
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37
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38 <stdio>
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39 <regex match=".*" source="both" level="log" description="tool progress"/>
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40 </stdio>
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41
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42 <tests>
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43 <!-- Cannot specify multiple repeats in test framework right now, so no tests possible. -->
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44 </tests>
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45
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46 <help>
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47 Please see the VCFtools `documentation`__ for help and further information.
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48
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49 .. __: http://vcftools.sourceforge.net/docs.html
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50 </help>
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51 </tool>