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annotate vcfdistance.xml @ 0:77ae7fbde89a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:31:21 -0500
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77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="vcfdistance" name="VCFdistance:" version="0.0.3">
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <description>Calculate distance to the nearest variant</description>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 <macros>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 <import>macros.xml</import>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 </macros>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 <expand macro="requirements"></expand>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 <expand macro="stdio" />
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 <command>cat "${input1}" | vcfdistance > "${out_file1}"</command>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 <inputs>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 </inputs>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 <outputs>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 <data format="vcf" name="out_file1" />
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 </outputs>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 <tests>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 <test>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 <param name="input1" value="vcflib.vcf"/>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 <output name="out_file1" file="vcfdistance-test1.vcf"/>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 </test>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 </tests>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 <help>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 Adds a value to each VCF record indicating the distance to the nearest variant in the file.
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 .. class:: infomark
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 The dataset used as input to this tool must be coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order).
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 ----
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 Vcfdistance @IS_PART_OF_VCFLIB@
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 </help>
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 <expand macro="citations" />
77ae7fbde89a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 </tool>