annotate vcfdistance.xml @ 1:ff5c6635c9a8

Updated to vcflib 86723982aa
author Anton Nekrutenko <anton@bx.psu.edu>
date Wed, 25 Jun 2014 16:14:03 -0400
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1 <tool id="vcfdistance" name="VCFdistance:" version="0.0.1">
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2 <requirements>
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ff5c6635c9a8 Updated to vcflib 86723982aa
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3 <requirement type="package" version="86723982aa">vcflib</requirement>
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4 </requirements>
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5 <description>Calculate distance to the nearest variant</description>
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6 <command>cat "${input1}" | vcfdistance > "${out_file1}"</command>
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7 <inputs>
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8 <param format="vcf" name="input1" type="data" label="First dataset"/>
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9 </inputs>
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10 <outputs>
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11 <data format="vcf" name="out_file1" />
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12 </outputs>
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13 <tests>
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14 <test>
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15 <param name="input1" value="vcflib.vcf"/>
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16 <output name="out_file1" file="vcfdistance-test1.vcf"/>
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17 </test>
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18 </tests>
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19 <help>
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21 Adds a value to each VCF record indicating the distance to the nearest variant in the file.
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23 .. class:: infomark
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25 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).
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27 ----
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28
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29 Vcfdistance is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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30
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31 </help>
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32 </tool>