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annotate vcffixup.xml @ 1:7951d68a5de5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:03:55 -0400
parents d9ead2da3182
children e88f38aa4040
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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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1 <tool id="vcffixup" name="VCFfixup:" version="@WRAPPER_VERSION@.0">
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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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
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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
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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"/>
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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
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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
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9 <inputs>
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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
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11 </inputs>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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12 <outputs>
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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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15 <tests>
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16 <test>
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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
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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>
7951d68a5de5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 <help>
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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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>