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comparison snpSift_vcfCheck.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
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0:9e8280e19338 1:98708b88af9f
1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0"> 1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0">
2 <description>basic checks for Vcf specification compliance</description> 2 <description>basic checks for Vcf specification compliance</description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>snpSift_macros.xml</import> 4 <import>snpSift_macros.xml</import>
6 </macros> 5 </macros>
7 <command> 6 <expand macro="requirements" />
8 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output 7 <expand macro="stdio" />
8 <expand macro="version_command" />
9 <command><![CDATA[
10 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
11 ]]>
9 </command> 12 </command>
10 <inputs> 13 <inputs>
11 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/> 14 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/>
12 </inputs> 15 </inputs>
13 <outputs> 16 <outputs>
14 <data format="vcf" name="output" /> 17 <data format="vcf" name="output" />
15 </outputs> 18 </outputs>
16 <expand macro="stdio" />
17 <tests> 19 <tests>
18 <test> 20 <test>
19 <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/> 21 <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/>
20 <output name="output"> 22 <output name="output">
21 <assert_contents> 23 <assert_contents>
22 <has_text text="Errors" /> 24 <has_text text="Errors" />
23 </assert_contents> 25 </assert_contents>
24 </output> 26 </output>
25 </test> 27 </test>
26 </tests> 28 </tests>
27 <help> 29 <help><![CDATA[
28 30
29 Perform some basic check ups on VCF files to spot common problems. 31 Perform some basic check ups on VCF files to spot common problems.
30 32
31 SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool. 33 SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool.
32 34
33 @EXTERNAL_DOCUMENTATION@ 35 @EXTERNAL_DOCUMENTATION@
34 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck 36 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
35 37
36 @CITATION_SECTION@ 38 ]]>
37
38 </help> 39 </help>
40 <expand macro="citations" />
39 </tool> 41 </tool>