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annotate vcfflatten.xml @ 2:5f4be9e020d9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author iuc
date Mon, 26 Mar 2018 12:14:07 -0400
parents 5fe607441f62
children 8b10da6b8026
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5f4be9e020d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
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1 <tool id="vcfflatten2" name="VCFflatten:" version="@WRAPPER_VERSION@+galaxy0">
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5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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2 <description>Removes multi-allelic sites by picking the most common alternate</description>
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devteam
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3 <macros>
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devteam
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4 <import>macros.xml</import>
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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5 </macros>
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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6 <expand macro="requirements"/>
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7 <expand macro="stdio" />
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8 <command>vcfflatten "${input1}" > "${out_file1}"</command>
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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9 <inputs>
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devteam
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10 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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11 </inputs>
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devteam
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12 <outputs>
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devteam
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13 <data format="vcf" name="out_file1" />
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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14 </outputs>
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devteam
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15 <tests>
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16 <test>
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17 <param name="input1" value="vcfflatten-input1.vcf"/>
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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18 <output name="out_file1" file="vcfflatten-test1.vcf"/>
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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19 </test>
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devteam
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20 </tests>
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21 <help>
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5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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23 Removes multi-allelic sites by picking the most common alternate. Requires allele frequency specification 'AF' and use of 'G' and 'A' to specify the fields which vary according to the Allele or Genotype.
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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25 ----
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5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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27 Vcfflatten @IS_PART_OF_VCFLIB@
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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28 </help>
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29 <expand macro="citations" />
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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30 </tool>