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comparison snpSift_int.xml @ 2:bf8c1526871b 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 12:11:18 -0500
parents 98708b88af9f
children 20c7d583fec1
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1:98708b88af9f 2:bf8c1526871b
1 <tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.1">
2 <description>Filter variants using intervals</description> 2 <description>Filter variants using intervals</description>
3 <!-- 3 <!--
4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
5 --> 5 -->
6 <macros> 6 <macros>
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output" 13 @CONDA_SNPSIFT_JAR_PATH@ &&
14 java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output"
14 ]]> 15 ]]>
15 </command> 16 </command>
16 <inputs> 17 <inputs>
17 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 18 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
18 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> 19 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>