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annotate vcfsort.xml @ 0:59d4413e75eb draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:34:33 -0500
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59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="vcfsort" name="VCFsort:" version="0.0.2">
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <description>Sort VCF dataset by coordinate</description>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 <command>(grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"</command>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 <inputs>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 </inputs>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 <outputs>
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8 <data format="vcf" name="out_file1" />
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 </outputs>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 <tests>
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11 <test>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 <param name="input1" value="vcfsort-test1-input.vcf"/>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 <output name="out_file1" file="vcfsort-test1.vcf"/>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 </test>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 </tests>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 <help>
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59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is::
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 .. class:: infomark
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 The same result can be achieved with the Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order).
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 </help>
59d4413e75eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 </tool>