Mercurial > repos > iuc > snpeff
comparison snpEff_download.xml @ 17:65ae79bddc69 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
author | iuc |
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date | Thu, 06 Sep 2018 13:23:57 -0400 |
parents | 5a29ab10dba6 |
children |
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16:c9ecd2a96ecf | 17:65ae79bddc69 |
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1 <tool id="snpEff_download" name="SnpEff download:" version="@wrapper_version@.galaxy1"> | 1 <tool id="snpEff_download" name="SnpEff download:" version="@WRAPPER_VERSION@.galaxy2"> |
2 <description> download a pre-built database</description> | 2 <description> download a pre-built database</description> |
3 <macros> | 3 <macros> |
4 <import>snpEff_macros.xml</import> | 4 <import>snpEff_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <requirements> | 6 <requirements> |
7 <expand macro="requirement" /> | 7 <expand macro="requirement" /> |
8 </requirements> | 8 </requirements> |
9 <expand macro="stdio" /> | 9 <expand macro="stdio" /> |
10 <expand macro="version_command" /> | 10 <expand macro="version_command" /> |
11 <command><![CDATA[ | 11 <command><![CDATA[ |
12 snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version' | 12 snpEff download -dataDir "\$PWD/temp" -v '$genome_version' && |
13 mkdir -p '$snpeff_db.files_path' && | |
14 mv temp/'$genome_version' '$snpeff_db.files_path' | |
13 ]]></command> | 15 ]]></command> |
14 <inputs> | 16 <inputs> |
15 <param name="genome_version" type="text" value="" label="Select the annotation database you want to download (e.g. GRCh38.86, mm10 etc.)" help="The list of available databases can be obtained with 'SnpEff databases' tool"> | 17 <param name="genome_version" type="text" value="" label="Select the annotation database you want to download (e.g. GRCh38.86, mm10 etc.)" help="The list of available databases can be obtained with 'SnpEff databases' tool"> |
16 <help>@snpeff_database_url@</help> | 18 <validator type="empty_field" message="A genome version name is required" /> |
17 <validator type="regex" message="A genome version name is required">\S+</validator> | |
18 </param> | 19 </param> |
19 </inputs> | 20 </inputs> |
20 <outputs> | 21 <outputs> |
21 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @snpeff_version@ ${genome_version}"/> | 22 <data name="snpeff_db" format="snpeffdb" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}"/> |
22 </outputs> | 23 </outputs> |
23 <tests> | 24 <tests> |
24 <test> | 25 <test> |
25 <param name="genome_version" value="ebola_zaire"/> | 26 <param name="genome_version" value="ebola_zaire"/> |
26 <output name="snpeff_db"> | 27 <output name="snpeff_db"> |
27 <assert_contents> | 28 <assert_contents> |
28 <has_text text="ebola_zaire" /> | 29 <has_text text="ebola_zaire" /> |
29 </assert_contents> | 30 </assert_contents> |
30 </output> | 31 </output> |
31 </test> | 32 </test> |
33 <test> | |
34 <param name="genome_version" value="Bdellovibrio_bacteriovorus_hd100"/> | |
35 <output name="snpeff_db"> | |
36 <assert_contents> | |
37 <has_text text="Bdellovibrio_bacteriovorus_hd100" /> | |
38 </assert_contents> | |
39 </output> | |
40 </test> | |
32 </tests> | 41 </tests> |
33 <help><![CDATA[ | 42 <help><![CDATA[ |
34 | |
35 **What it does** | 43 **What it does** |
36 | 44 |
37 This tool downloads a specified database from @snpeff_database_url@. It deposits it into the history. | 45 This tool downloads a specified database from @SNPEFF_DATABASE_URL@. It deposits it into the history. |
38 | 46 |
39 ------- | 47 ------- |
40 | 48 |
41 .. class:: infomark | 49 .. class:: infomark |
42 | 50 |
45 Suppose you want to annoate a VCF file containing variants within mm10 version of the Mouse genome. To do this you can: | 53 Suppose you want to annoate a VCF file containing variants within mm10 version of the Mouse genome. To do this you can: |
46 | 54 |
47 #. Download mm10 snpEff database by typing *mm10* into **Select the annotation database...** text box. | 55 #. Download mm10 snpEff database by typing *mm10* into **Select the annotation database...** text box. |
48 #. Use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter. | 56 #. Use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter. |
49 | 57 |
50 @snpeff_in_galaxy_info@ | 58 @SNPEFF_IN_GALAXY_INFO@ |
51 @external_documentation@ | 59 @EXTERNAL_DOCUMENTATION@ |
52 ]]></help> | 60 ]]></help> |
53 <expand macro="citations" /> | 61 <expand macro="citations" /> |
54 </tool> | 62 </tool> |