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1 <tool id="snpSift_int" name="SnpSift Intervals" version="3.3">
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2 <description>Filter variants using intervals </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 -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
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12 </command>
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13 <inputs>
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14 <param format="vcf" name="input" type="data" label="VCF input"/>
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15 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
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16 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals"
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17 help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
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18 </inputs>
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19 <outputs>
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20 <data format="vcf" name="output" />
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21 </outputs>
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22 <stdio>
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23 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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24 <exit_code range="1:" level="fatal" description="Error" />
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25 </stdio>
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26 <tests>
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27
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28 <test>
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29 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
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30 <param name="bedFile" ftype="bed" value="interval.bed"/>
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31 <param name="exclude" value="False"/>
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32 <output name="output">
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33 <assert_contents>
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34 <has_text text="872687" />
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35 <not_has_text text="1195966" />
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36 </assert_contents>
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37 </output>
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38 </test>
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39
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40 <test>
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41 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
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42 <param name="bedFile" ftype="bed" value="interval.bed"/>
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43 <param name="exclude" value="True"/>
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44 <output name="output">
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45 <assert_contents>
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46 <has_text text="1195966" />
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47 <not_has_text text="872687" />
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48 </assert_contents>
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49 </output>
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50 </test>
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51
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52 </tests>
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53
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54 <help>
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55
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56 You can filter using intervals (BED file)
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57
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58 For details about this tool, read the fine manual_ http://snpeff.sourceforge.net/SnpSift.html#intervals
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59
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60 For details about this tool, please see the snpEff_ web site.
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61
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62 .. _snpEff: http://snpEff.sourceforge.net
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63 .. _manual: http://snpeff.sourceforge.net/SnpSift.html#intervals
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64 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
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65 </help>
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66 </tool>
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