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annotate vcfsort.xml @ 3:5b7120c66efc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author iuc
date Mon, 26 Mar 2018 12:28:53 -0400
parents a8c5440d69e3
children f0580efedada
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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
diff changeset
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>
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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6 <command><![CDATA[
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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7 (grep ^"#" "${input1}" && grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${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
8 ]]></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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9 <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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10 <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
11 </inputs>
5b7120c66efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 2
diff changeset
12 <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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13 <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
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14 </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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15 <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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16 <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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17 <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
diff changeset
18 <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
diff changeset
19 </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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20 </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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21 <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
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22 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
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24 (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
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
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26 .. class:: infomark
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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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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28 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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29 </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
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30 </tool>