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annotate vcfgenotypes.xml @ 2:f5653ed90dfd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author iuc
date Mon, 26 Mar 2018 12:26:49 -0400
parents 82635a34fbe6
children a60ae8af21a1
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f5653ed90dfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
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1 <tool id="vcfgenotypes" name="VCFgenotypes:" version="@WRAPPER_VERSION@+galaxy0">
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82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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2 <description>Convert numerical representation of genotypes to allelic</description>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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3 <macros>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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4 <import>macros.xml</import>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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5 </macros>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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6 <expand macro="requirements"/>
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devteam
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7 <expand macro="stdio" />
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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8 <command>vcfgenotypes "${vcf_input}" > "${out_file1}"</command>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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9 <inputs>
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devteam
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10 <param format="vcf" name="vcf_input" type="data" label="Select VCF dataset"/>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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11 </inputs>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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12 <outputs>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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13 <data format="tabular" name="out_file1" />
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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14 </outputs>
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devteam
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15 <tests>
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16 <test>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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17 <param name="vcf_input" value="vcflib.vcf"/>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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18 <output name="out_file1" file="vcfgenotypes-test1.tab"/>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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19 </test>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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20 </tests>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 <help>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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23 Converts numerical representation of genotypes (standard in GT field) to the alleles provided in the call's ALT/REF fields.
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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25 ----
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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27 Vcfgenotypes @IS_PART_OF_VCFLIB@
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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28 </help>
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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29 <expand macro="citations" />
82635a34fbe6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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30 </tool>