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1 <tool id="vcftools_annotate" name="Annotate" version="0.1">
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2 <description>a VCF dataset with custom filters</description>
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3
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4 <requirements>
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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 <requirement type="set_environment">PERL5LIB</requirement>
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8 </requirements>
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9
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10 <command>
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11 ## Generate filter file.
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12 echo "{ tag => '${tag}', name => '${filter}', desc => '${description}', test => sub { my @t = split('%', @\\$MATCH[0]); return @t[0] $condition ? \\$PASS : \\$FAIL }, }," > f.txt ;
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13
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14 ## Annotate.
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15 vcf-annotate -f f.txt ${input} > ${output}
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16 </command>
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17 <inputs>
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18 <param name="input" label="Input" type="data" format="vcf"/>
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19 <param name="tag" label="Tag name" type="text"/>
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20 <param name="description" label="Tag description" type="text">
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21 <sanitizer sanitize="False"/>
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22 </param>
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23 <param name="filter" label="Filter name" type="text"/>
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24 <param name="condition" label="Filter condition" type="text">
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25 <sanitizer sanitize="False"/>
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26 </param>
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27 </inputs>
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28
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29 <outputs>
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30 <data name="output" format="vcf"/>
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31 </outputs>
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32
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33 <stdio>
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34 <regex match=".*" source="both" level="log" description="tool progress"/>
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35 </stdio>
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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="test_in1.vcf" />
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40 <param name="tag" value="FORMAT/FREQ" />
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41 <param name="description" value="MinAF [7]"/>
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42 <param name="filter" value="MinAF" />
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43 <param name="condition" value=">= 7" />
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44 <!-- 2 lines diff because command line with full file path is included in output VCF, and
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45 it not possible to match full file path. -->
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46 <output name="output" file="test_out1.vcf" lines_diff="2" />
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47 </test>
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48 </tests>
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49
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50 <help>
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51 Annotates VCF dataset with custom annotations. For example, if this format tag is used for allele frequency:
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52
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53 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
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54
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55 you can add a filter for allele frequency using "FORMAT/FREQ" as the tag name and the condition ">= [desired allele freq]"
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56
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57 Please see the VCFtools `documentation`__ for help and further information.
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58
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59 .. __: http://vcftools.sourceforge.net/perl_module.html#vcf-annotate
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60 </help>
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61 </tool>
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