Mercurial > repos > iuc > snpsift

annotate snpSift_int.xml @ 3:20c7d583fec1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:32 -0400
parents bf8c1526871b
children 09d6806c609e
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20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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 SnpSift -Xmx2G intervals
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14 -i '$input'
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15 $exclude
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16 '$bedFile'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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17 > '$output'
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18 ]]></command>
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19 <inputs>
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20 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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21 <param name="bedFile" type="data" format="bed" label="Intervals (BED file)"/>
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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22 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals"
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23 help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
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24 </inputs>
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25 <outputs>
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26 <data name="output" format="vcf" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
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31 <param name="bedFile" ftype="bed" value="interval.bed"/>
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32 <param name="exclude" value="False"/>
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33 <output name="output">
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34 <assert_contents>
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35 <has_text text="872687" />
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36 <not_has_text text="1195966" />
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37 </assert_contents>
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38 </output>
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39 </test>
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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 </tests>
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52 <help><![CDATA[
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53 You can filter using intervals (BED file).
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54
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55 @EXTERNAL_DOCUMENTATION@
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56 - http://snpeff.sourceforge.net/SnpSift.html#intervals
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57 ]]></help>
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58 <expand macro="citations" />
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59 </tool>