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1 <tool id="vcftools_slice" name="Slice VCF" version="0.1">
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2 <description>to get data from selected regions</description>
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3
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4 <requirements>
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1
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5 <requirement type="binary">echo</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 ## Only works if input is sorted.
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11 vcf-sort ${input} > sorted.vcf
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12
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13 ## As of v0.1.10, the first line of a BED file is assumed to be a header and ignored,
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14 ## so add a dummy header line if necessary.
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15 #set first_line = open( str($regions) ).readline()
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16 #if first_line.startswith( '#' ):
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17 ## Header already exists, so just link.
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18 ; ln -s $regions regions.bed
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19 #else:
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20 ## Add dummy header.
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21 ; echo '#dummy header' | cat - $regions > regions.bed
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22 #end if
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23
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24 ## Slice VCF.
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25 ; vcftools --vcf sorted.vcf --out output --bed regions.bed --recode
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26 </command>
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27
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28 <inputs>
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29 <param name="input" label="Input dataset" type="data" format="vcf"/>
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30 <param name="regions" label="Regions" type="data" format="bed"/>
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31 </inputs>
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32
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33 <outputs>
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34 <data name="output" format="vcf" from_work_dir="output.recode.vcf"/>
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35 </outputs>
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36
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37 <tests>
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38 <test>
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39 <param name="input" value="slice_in.vcf"/>
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40 <param name="regions" value="regions.bed"/>
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41 <output name="output" file="slice_out.vcf"/>
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42 </test>
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43 </tests>
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44
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45 <help>
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46 Please see the VCFtools `documentation`__ for help and further information.
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47
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48 .. __: http://vcftools.sourceforge.net/docs.html
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49 </help>
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50 </tool>
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