annotate vcfdistance.xml @ 1:48e458c721b3 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:05:01 -0400
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48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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1 <tool id="vcfdistance" name="VCFdistance:" version="@WRAPPER_VERSION@.0">
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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2 <description>Calculate distance to the nearest variant</description>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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3 <macros>
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4 <import>macros.xml</import>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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5 </macros>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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6 <expand macro="requirements"/>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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7 <expand macro="stdio" />
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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8 <command>cat "${input1}" | vcfdistance > "${out_file1}"</command>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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9 <inputs>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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10 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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11 </inputs>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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12 <outputs>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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13 <data format="vcf" name="out_file1" />
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance 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"/>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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18 <output name="out_file1" file="vcfdistance-test1.vcf"/>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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19 </test>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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20 </tests>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 <help>
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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23 Adds a value to each VCF record indicating the distance to the nearest variant in the file.
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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25 .. class:: infomark
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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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).
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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29 ----
48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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48e458c721b3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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31 Vcfdistance @IS_PART_OF_VCFLIB@
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32 </help>
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33 <expand macro="citations" />
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34 </tool>