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annotate vcfflatten.xml @ 0:ac725e729ac6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:32:13 -0500
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children 5fe607441f62
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ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="vcfflatten2" name="VCFflatten:" version="0.0.3">
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <description>Removes multi-allelic sites by picking the most common alternate</description>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 <macros>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 <import>macros.xml</import>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 </macros>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 <expand macro="requirements"></expand>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 <expand macro="stdio" />
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 <command>vcfflatten "${input1}" > "${out_file1}"</command>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 <inputs>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 </inputs>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 <outputs>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 <data format="vcf" name="out_file1" />
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 </outputs>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 <tests>
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16 <test>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 <param name="input1" value="vcfflatten-input1.vcf"/>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 <output name="out_file1" file="vcfflatten-test1.vcf"/>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 </test>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 </tests>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 <help>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 Removes multi-allelic sites by picking the most common alternate. Requires allele frequency specification 'AF' and use of 'G' and 'A' to specify the fields which vary according to the Allele or Genotype.
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 ----
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 Vcfflatten @IS_PART_OF_VCFLIB@
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 </help>
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 <expand macro="citations" />
ac725e729ac6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 </tool>