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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit f28d66c0bcad8ac29be2afec28bc639317239775
author iuc
date Tue, 01 Oct 2024 13:48:21 +0000
parents dd44c3f416c3
children
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5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
diff changeset
1 <tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@+galaxy0">
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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2 <description>Sort VCF dataset by coordinate</description>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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3 <macros>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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4 <import>macros.xml</import>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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5 </macros>
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dd44c3f416c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit 9a0c41967765d120a8fc519c0c7f09cbe3a6efbe"
iuc
parents: 4
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6 <requirements>
dd44c3f416c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit 9a0c41967765d120a8fc519c0c7f09cbe3a6efbe"
iuc
parents: 4
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7 <requirement type="package" version="8.31">coreutils</requirement>
dd44c3f416c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit 9a0c41967765d120a8fc519c0c7f09cbe3a6efbe"
iuc
parents: 4
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8 </requirements>
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5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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9 <command><![CDATA[
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f0580efedada "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 3
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10 (grep ^"#" "${input1}" && grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > '${out_file1}'
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5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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11 ]]></command>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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12 <inputs>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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13 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
diff changeset
14 </inputs>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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15 <outputs>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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16 <data format="vcf" name="out_file1" />
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
diff changeset
17 </outputs>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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18 <tests>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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19 <test>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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20 <param name="input1" value="vcfsort-test1-input.vcf"/>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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21 <output name="out_file1" file="vcfsort-test1.vcf"/>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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22 </test>
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40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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23 </tests>
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5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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24 <help>
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40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
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25 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
devteam
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40296713cd82 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
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27 (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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29 .. 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
devteam
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31 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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5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
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32 </help>
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ee60203e68d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit f28d66c0bcad8ac29be2afec28bc639317239775
iuc
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33 <expand macro="citations" />
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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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34 </tool>