annotate snpSift_int.xml @ 7:b26a1aff7f81

Fix issues with snpEff commandline template and add test cases
author Jim Johnson <jj@umn.edu>
date Thu, 28 Mar 2013 12:29:45 -0500
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1 <tool id="snpSift_int" name="SnpSift Intervals" version="3.1">
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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="3.1">snpEff</requirement>
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9 </requirements>
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10 <command>
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11 cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $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 </inputs>
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17 <outputs>
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18 <data format="vcf" name="output" />
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19 </outputs>
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20 <stdio>
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21 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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22 <exit_code range="1:" level="fatal" description="Error" />
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23 </stdio>
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24 <tests>
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25 <test>
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26 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
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27 <param name="bedFile" ftype="bed" value="interval.bed"/>
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28 <output name="output">
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29 <assert_contents>
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30 <has_text text="872687" />
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31 <not_has_text text="1195966" />
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32 </assert_contents>
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33 </output>
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34 </test>
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35
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36 </tests>
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37
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38 <help>
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39
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40 You can filter using intervals (BED file)
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41
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42 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
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43
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44 </help>
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45 </tool>