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1 <tool id="vcftools_isec" name="Intersect" 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 ## Intersect.
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26 vcf-isec -f
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27 #if $complement:
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28 -c
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29 #end if
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30 #echo ' '.join( dataset_names ) # > ${output}
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31 </command>
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32 <inputs>
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33 <repeat name="inputs" title="Dataset" min="2">
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34 <param name="file" label="Dataset" type="data" format="vcf"/>
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35 </repeat>
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36 <param name="complement" type="boolean" label="Complement intersection" help="If checked, output positions present in the first file but missing from the other files"/>
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37 </inputs>
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38
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39 <outputs>
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40 <data name="output" format="vcf"/>
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41 </outputs>
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42
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43 <stdio>
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44 <regex match=".*" source="both" level="log" description="tool progress"/>
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45 </stdio>
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46
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47 <tests>
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48 <!-- Cannot specify multiple repeats in test framework right now.
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49 <test>
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50 <param name='inputs|1' value='1.vcf' />
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51 <param name='inputs|2' value='2.vcf' />
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52 <param name='complement' value='False' />
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53 <output name='output' file='out.vcf' />
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54 </test>
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55 -->
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56 </tests>
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57
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58 <help>
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59 Please see the VCFtools `documentation`__ for help and further information.
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60
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61 .. __: http://vcftools.sourceforge.net/docs.html
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62 </help>
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63 </tool>
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