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comparison snpEff_download.xml @ 17:65ae79bddc69 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
author iuc
date Thu, 06 Sep 2018 13:23:57 -0400
parents 5a29ab10dba6
children
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16:c9ecd2a96ecf 17:65ae79bddc69
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>