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annotate vcfflatten.xml @ 2:b24e368ae7b1 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 12:25:46 -0400
parents 1336a70f5c02
children f285aa6bdcfb
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b24e368ae7b1 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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1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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2 <description>Removes multi-allelic sites by picking the most common alternate</description>
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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3 <macros>
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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4 <import>macros.xml</import>
1336a70f5c02 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>
1336a70f5c02 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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devteam
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7 <expand macro="stdio" />
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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8 <command>vcfflatten "${input1}" > "${out_file1}"</command>
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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9 <inputs>
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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10 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
1336a70f5c02 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>
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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12 <outputs>
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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13 <data format="vcf" name="out_file1" />
1336a70f5c02 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>
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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15 <tests>
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16 <test>
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devteam
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17 <param name="input1" value="vcfflatten-input1.vcf"/>
1336a70f5c02 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"/>
1336a70f5c02 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>
1336a70f5c02 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>
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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21 <help>
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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1336a70f5c02 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.
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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25 ----
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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1336a70f5c02 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@
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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28 </help>
1336a70f5c02 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" />
1336a70f5c02 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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30 </tool>