Mercurial > repos > iuc > snpsift

annotate snpSift_int.xml @ 14:80da7fae14b8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:10:54 -0500
parents ed810da439cc
children 8bd645802765
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80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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1 <tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.1">
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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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b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
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9 <expand macro="requirements" />
b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
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10 <expand macro="stdio" />
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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11 <expand macro="version_command" />
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12 <command><![CDATA[
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80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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13 @CONDA_SNPSIFT_JAR_PATH@ &&
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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14 java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output"
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
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19 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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20 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals"
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21 help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
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22 </inputs>
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23 <outputs>
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24 <data format="vcf" name="output" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
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29 <param name="bedFile" ftype="bed" value="interval.bed"/>
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30 <param name="exclude" value="False"/>
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31 <output name="output">
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32 <assert_contents>
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33 <has_text text="872687" />
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34 <not_has_text text="1195966" />
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35 </assert_contents>
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36 </output>
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37 </test>
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38 <test>
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39 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
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40 <param name="bedFile" ftype="bed" value="interval.bed"/>
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41 <param name="exclude" value="True"/>
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42 <output name="output">
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43 <assert_contents>
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44 <has_text text="1195966" />
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45 <not_has_text text="872687" />
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46 </assert_contents>
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47 </output>
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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51
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52 You can filter using intervals (BED file).
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53
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54 @EXTERNAL_DOCUMENTATION@
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55 http://snpeff.sourceforge.net/SnpSift.html#intervals
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56
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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57 ]]>
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58 </help>
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59 <expand macro="citations" />
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60 </tool>