Mercurial > repos > iuc > snpsift

comparison snpSift_vcfCheck.xml @ 3:20c7d583fec1 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 fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:32 -0400
parents bf8c1526871b
children 09d6806c609e
comparison
equal deleted inserted replaced
2:bf8c1526871b 3:20c7d583fec1
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>