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comparison snpSift_int.xml @ 1:98708b88af9f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author iuc
date Tue, 07 Jun 2016 10:04:09 -0400
parents 9e8280e19338
children bf8c1526871b
comparison
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0:9e8280e19338 1:98708b88af9f
1 <tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0"> 1 <tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0">
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 <expand macro="requirements" />
7 <macros> 6 <macros>
8 <import>snpSift_macros.xml</import> 7 <import>snpSift_macros.xml</import>
9 </macros> 8 </macros>
10 <command> 9 <expand macro="requirements" />
11 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output 10 <expand macro="stdio" />
11 <expand macro="version_command" />
12 <command><![CDATA[
13 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output"
14 ]]>
12 </command> 15 </command>
13 <inputs> 16 <inputs>
14 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 17 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
15 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> 18 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
16 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" 19 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals"
17 help="Filter out (exclude) VCF entries that match any interval in the BED files"/> 20 help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
18 </inputs> 21 </inputs>
19 <outputs> 22 <outputs>
20 <data format="vcf" name="output" /> 23 <data format="vcf" name="output" />
21 </outputs> 24 </outputs>
22 <expand macro="stdio" />
23 <tests> 25 <tests>
24 <test> 26 <test>
25 <param name="input" ftype="vcf" value="annotate_5.vcf"/> 27 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
26 <param name="bedFile" ftype="bed" value="interval.bed"/> 28 <param name="bedFile" ftype="bed" value="interval.bed"/>
27 <param name="exclude" value="False"/> 29 <param name="exclude" value="False"/>
42 <not_has_text text="872687" /> 44 <not_has_text text="872687" />
43 </assert_contents> 45 </assert_contents>
44 </output> 46 </output>
45 </test> 47 </test>
46 </tests> 48 </tests>
47 <help> 49 <help><![CDATA[
48 50
49 You can filter using intervals (BED file). 51 You can filter using intervals (BED file).
50 52
51 @EXTERNAL_DOCUMENTATION@ 53 @EXTERNAL_DOCUMENTATION@
52 http://snpeff.sourceforge.net/SnpSift.html#intervals 54 http://snpeff.sourceforge.net/SnpSift.html#intervals
53 55
54 @CITATION_SECTION@ 56 ]]>
55
56 </help> 57 </help>
58 <expand macro="citations" />
57 </tool> 59 </tool>