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annotate vcffixup.xml @ 0:d9ead2da3182 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:31:56 -0500
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children 7951d68a5de5
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d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="vcffixup" name="VCFfixup:" version="0.0.3">
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <description>Count the allele frequencies across alleles present in each record in the VCF file</description>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 <macros>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 <import>macros.xml</import>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 </macros>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 <expand macro="requirements"></expand>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 <expand macro="stdio" />
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 <command>vcffixup "${input1}" > "${out_file1}"</command>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 <inputs>
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10 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 </inputs>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 <outputs>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 <data format="vcf" name="out_file1" />
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 </outputs>
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15 <tests>
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16 <test>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 <param name="input1" value="vcflib.vcf"/>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 <output name="out_file1" file="vcffixup-test1.vcf"/>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 </test>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 </tests>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 <help>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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.
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 ----
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 Vcffixup @IS_PART_OF_VCFLIB@
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 </help>
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 <expand macro="citations" />
d9ead2da3182 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 </tool>