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1 <tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0">
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2 <description>Filter variants using intervals</description>
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3 <!--
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4 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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5 -->
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6 <macros>
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7 <import>snpSift_macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version_command" />
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12 <command><![CDATA[
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13 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
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18 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
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19 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals"
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20 help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
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21 </inputs>
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22 <outputs>
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23 <data format="vcf" name="output" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
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28 <param name="bedFile" ftype="bed" value="interval.bed"/>
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29 <param name="exclude" value="False"/>
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30 <output name="output">
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31 <assert_contents>
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32 <has_text text="872687" />
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33 <not_has_text text="1195966" />
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34 </assert_contents>
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35 </output>
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36 </test>
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37 <test>
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38 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
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39 <param name="bedFile" ftype="bed" value="interval.bed"/>
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40 <param name="exclude" value="True"/>
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41 <output name="output">
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42 <assert_contents>
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43 <has_text text="1195966" />
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44 <not_has_text text="872687" />
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45 </assert_contents>
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46 </output>
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50
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51 You can filter using intervals (BED file).
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52
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53 @EXTERNAL_DOCUMENTATION@
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54 http://snpeff.sourceforge.net/SnpSift.html#intervals
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55
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56 @CITATION_SECTION@
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57
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58 ]]>
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59 </help>
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60 </tool>
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