Mercurial > repos > iuc > snpsift

comparison snpSift_vcfCheck.xml @ 13:ed810da439cc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
author iuc
date Tue, 07 Jun 2016 09:41:13 -0400
parents b884686a80dc
children 80da7fae14b8
comparison
equal deleted inserted replaced
12:6bf58286d795 13:ed810da439cc
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 <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 <command> 8 <expand macro="version_command" />
9 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output 9 <command><![CDATA[
10 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
11 ]]>
10 </command> 12 </command>
11 <inputs> 13 <inputs>
12 <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"/>
13 </inputs> 15 </inputs>
14 <outputs> 16 <outputs>
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>