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1 <tool id="vcftools_compare" name="Compare" 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 $input in $inputs:
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13 ## Sort file.
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14 sort -k1,1 -k2,2n ${input.file} > ${input.name}.vcf.sorted ;
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15
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16 ## Compress.
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17 bgzip ${input.name}.vcf.sorted ;
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18
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19 ## Index.
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20 tabix -p vcf ${input.name}.vcf.sorted.gz ;
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21
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22 #silent dataset_names.append( str($input.name) + '.vcf.sorted.gz' )
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23 #end for
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24
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25 ## Compare and use sed to simplify output.
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26 vcf-compare -w ${window} ${ignore_indels} #echo ' '.join( dataset_names )# | sed 's/\.vcf\.sorted\.gz//g' > ${output}
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27 </command>
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28 <inputs>
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29 <repeat name="inputs" title="Datasets to Compare" min="2">
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30 <param name="name" label="Dataset name" type="text" />
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31 <param name="file" label="Dataset" type="data" format="vcf"/>
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32 </repeat>
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33 <param name="window" label="Comparison window" type="integer" min="0" value="0" help="In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a SNP or an indel)."/>
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34
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35 <param name="ignore_indels" label="Ignore indels" type="select" help="Exclude sites containing indels from genotype comparison">
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36 <option value="" selected="True">No</option>
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37 <option value="--ignore-indels">Yes</option>
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38 </param>
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39 </inputs>
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40
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41 <outputs>
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42 <data name="output" format="tabular"/>
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43 </outputs>
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44
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45 <stdio>
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46 <regex match=".*" source="both" level="log" description="tool progress"/>
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47 </stdio>
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48
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49 <tests>
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50 <!-- Cannot specify multiple repeats in test framework right now, so no tests possible. -->
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51 </tests>
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52
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53 <help>
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54 Please see the VCFtools `documentation`__ for help and further information.
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55
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56 .. __: http://vcftools.sourceforge.net/docs.html
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57 </help>
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58 </tool>
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