Mercurial > repos > devteam > vcfsort

annotate vcfsort.xml @ 5:4f148dd50583 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 13:48:08 +0000
parents 694dfc3f5d45
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
1 <tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@+galaxy0">
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
2 <description>Sort VCF dataset by coordinate</description>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
3 <macros>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
4 <import>macros.xml</import>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
5 </macros>
4
694dfc3f5d45 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit 9a0c41967765d120a8fc519c0c7f09cbe3a6efbe"
iuc
parents: 3
diff changeset
6 <requirements>
694dfc3f5d45 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit 9a0c41967765d120a8fc519c0c7f09cbe3a6efbe"
iuc
parents: 3
diff changeset
7 <requirement type="package" version="8.31">coreutils</requirement>
694dfc3f5d45 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit 9a0c41967765d120a8fc519c0c7f09cbe3a6efbe"
iuc
parents: 3
diff changeset
8 </requirements>
2
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
9 <command><![CDATA[
3
24f96edb5b29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
10 (grep ^"#" "${input1}" && grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > '${out_file1}'
2
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
11 ]]></command>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
12 <inputs>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
13 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
14 </inputs>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
15 <outputs>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
16 <data format="vcf" name="out_file1" />
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
17 </outputs>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
18 <tests>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
19 <test>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
20 <param name="input1" value="vcfsort-test1-input.vcf"/>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
21 <output name="out_file1" file="vcfsort-test1.vcf"/>
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
22 </test>
1
586f4536fc65 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
parents: 0
diff changeset
23 </tests>
2
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
24 <help>
1
586f4536fc65 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
parents: 0
diff changeset
25 This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is::
586f4536fc65 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
parents: 0
diff changeset
26
586f4536fc65 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
parents: 0
diff changeset
27 (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file
586f4536fc65 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
parents: 0
diff changeset
28
586f4536fc65 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
parents: 0
diff changeset
29 .. class:: infomark
586f4536fc65 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
parents: 0
diff changeset
30
586f4536fc65 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
parents: 0
diff changeset
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).
2
d92d6f631ff5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
32 </help>
5
4f148dd50583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit f28d66c0bcad8ac29be2afec28bc639317239775
iuc
parents: 4
diff changeset
33 <expand macro="citations" />
1
586f4536fc65 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
devteam
parents: 0
diff changeset
34 </tool>