Mercurial > repos > iuc > snpsift

annotate snpSift_vcfCheck.xml @ 14:80da7fae14b8 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 12:10:54 -0500
parents ed810da439cc
children 8bd645802765
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80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.1">
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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2 <description>basic checks for VCF specification compliance</description>
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3 <macros>
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4 <import>snpSift_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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8 <expand macro="version_command" />
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9 <command><![CDATA[
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10 @CONDA_SNPSIFT_JAR_PATH@ &&
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11 java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/>
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16 </inputs>
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17 <outputs>
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18 <data format="vcf" name="output" />
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19 </outputs>
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20 <tests>
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21 <test>
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80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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22 <param name="input" ftype="vcf" value="test_bad.vcf"/>
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23 <assert_stderr>
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24 <has_text text="Errors" />
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25 </assert_stderr>
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29 Perform some basic check ups on VCF files to spot common problems.
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30
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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.
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33 @EXTERNAL_DOCUMENTATION@
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34 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
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35 ]]>
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36 </help>
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37 <expand macro="citations" />
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38 </tool>