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1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.3">
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2 <description>Annotate SNPs from dbSnp</description>
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3 <!--
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4 You will need to change the path to wherever your installation is.
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5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
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6 -->
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7 <requirements>
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8 <requirement type="package" version="3.3">snpEff</requirement>
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9 </requirements>
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10 <command>
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11 java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar $annotate_cmd
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12 #if $annotate.id :
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13 -id
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14 #elif $annotate.info_ids.__str__.strip() != '' :
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15 -info "$annotate.info_ids"
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16 #end if
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17 -q $dbSnp $input > $output
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18 </command>
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19 <inputs>
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20 <param format="vcf" name="input" type="data" label="VCF input"/>
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21 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)"
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22 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
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23 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Annotate in Memory"
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24 help="allows unsorted VCF files, but it loads the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files)"/>
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25 <conditional name="annotate">
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26 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
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27 <when value="id"/>
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28 <when value="info">
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29 <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs"
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30 help="list is a comma separated list of fields. When blank, all INFO fields are included">
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31 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
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32 </param>
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33 </when>
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34 </conditional>
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35 </inputs>
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36 <stdio>
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37 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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38 <exit_code range="1:" level="fatal" description="Error" />
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39 </stdio>
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40
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41 <outputs>
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42 <data format="vcf" name="output" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
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47 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
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48 <param name="annotate_cmd" value="False"/>
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49 <param name="id" value="True"/>
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50 <output name="output">
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51 <assert_contents>
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52 <has_text text="rs76166080" />
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help>
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58
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59 This is typically used to annotate IDs from dbSnp.
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60
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61 For details about this tool, read the fine manual_ http://snpeff.sourceforge.net/SnpSift.html#annotate
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62
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63 For details about this tool, please see the snpEff_ web site.
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64
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65 .. _snpEff: http://snpEff.sourceforge.net
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66 .. _manual: http://snpeff.sourceforge.net/SnpSift.html#annotate
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67 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
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68
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69 </help>
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70 </tool>
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71
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