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1 <tool id="vcfsort" name="VCFsort:" version="0.0.1">
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2 <description>Sort VCF dataset by coordinate</description>
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3 <command>(grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"</command>
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4 <inputs>
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5 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
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6 </inputs>
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7 <outputs>
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8 <data format="vcf" name="out_file1" />
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9 </outputs>
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10 <tests>
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11 <test>
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12 <param name="input1" value="vcfsort-test1-input.vcf"/>
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13 <output name="out_file1" file="vcfsort-test1.vcf"/>
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14 </test>
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15 </tests>
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16 <help>
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17
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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::
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19
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20 (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file
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21
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22 .. class:: infomark
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23
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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).
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25
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26 </help>
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27 </tool>
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