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annotate vcffixup.xml @ 1:9d7e64e4b9fc 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 16:05:59 -0400
parents a03f346b6aae
children fc5a64fdd5b2
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9d7e64e4b9fc 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">
9d7e64e4b9fc 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>
9d7e64e4b9fc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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3 <macros>
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4 <import>macros.xml</import>
9d7e64e4b9fc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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5 </macros>
9d7e64e4b9fc 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" />
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8 <command>vcffixup "${input1}" > "${out_file1}"</command>
9d7e64e4b9fc 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"/>
9d7e64e4b9fc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup 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" />
9d7e64e4b9fc 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"/>
9d7e64e4b9fc 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"/>
9d7e64e4b9fc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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19 </test>
9d7e64e4b9fc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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20 </tests>
9d7e64e4b9fc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 <help>
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9d7e64e4b9fc 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.
9d7e64e4b9fc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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9d7e64e4b9fc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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25 ----
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9d7e64e4b9fc 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@
9d7e64e4b9fc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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28 </help>
9d7e64e4b9fc 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" />
9d7e64e4b9fc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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30 </tool>