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comparison snpSift_vcfCheck.xml @ 15:8bd645802765 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 10:24:36 -0400
parents 80da7fae14b8
children ede8954f5c82
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14:80da7fae14b8 15:8bd645802765
1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.1"> 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 <macros> 3 <macros>
4 <import>snpSift_macros.xml</import> 4 <import>snpSift_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command><![CDATA[ 9 <command><![CDATA[
10 @CONDA_SNPSIFT_JAR_PATH@ && 10 SnpSift -Xmx2G vcfCheck
11 java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output" 11 '$input'
12 ]]> 12 > '$output'
13 </command> 13 ]]></command>
14 <inputs> 14 <inputs>
15 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/> 15 <param name="input" type="data" format="vcf" label="Variant input file in VCF format to check"/>
16 </inputs> 16 </inputs>
17 <outputs> 17 <outputs>
18 <data format="vcf" name="output" /> 18 <data name="output" format="vcf" />
19 </outputs> 19 </outputs>
20 <tests> 20 <tests>
21 <test> 21 <test expect_exit_code="0">
22 <param name="input" ftype="vcf" value="test_bad.vcf"/> 22 <param name="input" ftype="vcf" value="test_bad.vcf"/>
23 <assert_stderr> 23 <assert_stderr>
24 <has_text text="Errors" /> 24 <has_text text="Errors" />
25 </assert_stderr> 25 </assert_stderr>
26 </test> 26 </test>
29 Perform some basic check ups on VCF files to spot common problems. 29 Perform some basic check ups on VCF files to spot common problems.
30 30
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. 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.
32 32
33 @EXTERNAL_DOCUMENTATION@ 33 @EXTERNAL_DOCUMENTATION@
34 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck 34 - http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
35 ]]> 35 ]]></help>
36 </help>
37 <expand macro="citations" /> 36 <expand macro="citations" />
38 </tool> 37 </tool>