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annotate vcffixup.xml @ 2:e88f38aa4040 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author iuc
date Mon, 26 Mar 2018 12:13:46 -0400
parents 7951d68a5de5
children 2dd8063bab3b
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e88f38aa4040 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
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1 <tool id="vcffixup" name="VCFfixup:" version="@WRAPPER_VERSION@+galaxy0">
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7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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2 <description>Count the allele frequencies across alleles present in each record in the VCF file</description>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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3 <macros>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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4 <import>macros.xml</import>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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5 </macros>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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6 <expand macro="requirements"/>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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7 <expand macro="stdio" />
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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8 <command>vcffixup "${input1}" > "${out_file1}"</command>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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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"/>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup 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" />
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup 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>
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devteam
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17 <param name="input1" value="vcflib.vcf"/>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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18 <output name="out_file1" file="vcffixup-test1.vcf"/>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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19 </test>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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20 </tests>
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21 <help>
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7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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23 Uses genotypes from the selected VCF dataset to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records.
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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25 ----
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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27 Vcffixup @IS_PART_OF_VCFLIB@
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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28 </help>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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29 <expand macro="citations" />
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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30 </tool>