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annotate vcfflatten.xml @ 1:5fe607441f62 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:04:07 -0400
parents ac725e729ac6
children 5f4be9e020d9
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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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1 <tool id="vcfflatten2" name="VCFflatten:" version="@WRAPPER_VERSION@.0">
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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3 <macros>
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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
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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
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6 <expand macro="requirements"/>
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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7 <expand macro="stdio" />
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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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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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
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11 </inputs>
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12 <outputs>
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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
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14 </outputs>
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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
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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
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19 </test>
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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20 </tests>
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 <help>
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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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 ----
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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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>
5fe607441f62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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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>