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comparison snpSift_vcfCheck.xml @ 2:bf8c1526871b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:11:18 -0500
parents 98708b88af9f
children 20c7d583fec1
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1:98708b88af9f 2:bf8c1526871b
1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.1">
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 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output" 10 @CONDA_SNPSIFT_JAR_PATH@ &&
11 java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
11 ]]> 12 ]]>
12 </command> 13 </command>
13 <inputs> 14 <inputs>
14 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/> 15 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/>
15 </inputs> 16 </inputs>
16 <outputs> 17 <outputs>
17 <data format="vcf" name="output" /> 18 <data format="vcf" name="output" />
18 </outputs> 19 </outputs>
19 <tests> 20 <tests>
20 <test> 21 <test>
21 <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/> 22 <param name="input" ftype="vcf" value="test_bad.vcf"/>
22 <output name="output"> 23 <assert_stderr>
23 <assert_contents> 24 <has_text text="Errors" />
24 <has_text text="Errors" /> 25 </assert_stderr>
25 </assert_contents>
26 </output>
27 </test> 26 </test>
28 </tests> 27 </tests>
29 <help><![CDATA[ 28 <help><![CDATA[
30
31 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.
32 30
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. 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.
34 32
35 @EXTERNAL_DOCUMENTATION@ 33 @EXTERNAL_DOCUMENTATION@
36 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck 34 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
37
38 ]]> 35 ]]>
39 </help> 36 </help>
40 <expand macro="citations" /> 37 <expand macro="citations" />
41 </tool> 38 </tool>