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annotate vcfsort.xml @ 2:a8c5440d69e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
author devteam
date Mon, 03 Oct 2016 11:23:06 -0400
parents 40296713cd82
children 5b7120c66efc
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40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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1 <tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@.0">
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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2 <description>Sort VCF dataset by coordinate</description>
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a8c5440d69e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
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3 <macros>
a8c5440d69e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
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4 <import>macros.xml</import>
a8c5440d69e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
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5 </macros>
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40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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6 <command>(grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"</command>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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7 <inputs>
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8 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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9 </inputs>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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10 <outputs>
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11 <data format="vcf" name="out_file1" />
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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12 </outputs>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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13 <tests>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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14 <test>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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15 <param name="input1" value="vcfsort-test1-input.vcf"/>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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16 <output name="out_file1" file="vcfsort-test1.vcf"/>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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17 </test>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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18 </tests>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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19 <help>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is::
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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23 (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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25 .. class:: infomark
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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27 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).
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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29 </help>
40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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30 </tool>