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comparison snpEff_databases.xml @ 12:5a29ab10dba6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
author iuc
date Thu, 29 Mar 2018 20:39:49 -0400
parents 5b4ac70948d2
children c9ecd2a96ecf
comparison
equal deleted inserted replaced
11:bfa6c1b8a03c 12:5a29ab10dba6
1 <tool id="snpEff_databases" name="SnpEff databases:" version="@wrapper_version@.1"> 1 <tool id="snpEff_databases" name="SnpEff databases:" version="@wrapper_version@.galaxy1">
2 <description> list available databases</description> 2 <description> list available databases</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>
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 12
13 snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' 13 snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g'
14 14
15 #if $include_pattern: 15 #if $include_pattern:
16 | grep '${include_pattern}' 16 | grep '${include_pattern}'
17 #end if 17 #end if
18 18
19 #if $exclude_pattern: 19 #if $exclude_pattern:
20 | grep -v '${exclude_pattern}' 20 | grep -v '${exclude_pattern}'
21 #end if 21 #end if
22 22
23 > '${snpeff_dbs}' 23 > '${snpeff_dbs}'
24 24
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <param name="include_pattern" size="40" type="text" value="" optional="True" label="List entries matching the following expression" help="Databases matching this expression will be listed. Here you can enter text or regular expression. For example, to show only mouse databases use 'Mouse'. Note that this parameter is case-sensitive."> 27 <param name="include_pattern" size="40" type="text" value="" optional="True" label="List entries matching the following expression" help="Databases matching this expression will be listed. Here you can enter text or regular expression. For example, to show only mouse databases use 'Mouse'. Note that this parameter is case-sensitive.">
28 <sanitizer> 28 <sanitizer>
29 <valid initial="string.digits,string.letters"> 29 <valid initial="string.digits,string.letters">
67 This tool downloads the master list of snpEff databases from @snpeff_database_url@. You can then look at this list and decide which database to use for your analysis. For example, if **List entries matching the following expression** parameter of this tool is set to *Mouse* the it will produce a tabular dataset with the following content:: 67 This tool downloads the master list of snpEff databases from @snpeff_database_url@. You can then look at this list and decide which database to use for your analysis. For example, if **List entries matching the following expression** parameter of this tool is set to *Mouse* the it will produce a tabular dataset with the following content::
68 68
69 mm10 Mouse http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm10.zip 69 mm10 Mouse http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm10.zip
70 mm9 Mouse http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm9.zip 70 mm9 Mouse http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm9.zip
71 71
72 This means that there two available snpEff databases for mouse genome versions mm9 and mm10. In order to download these databases you should use identifier from the first column (e.g., mm9 or mm10 in this case). 72 This means that there two available snpEff databases for mouse genome versions mm9 and mm10. In order to download these databases you should use identifier from the first column (e.g., mm9 or mm10 in this case).
73 73
74 ------- 74 -------
75 75
76 .. class:: infomark 76 .. class:: infomark
77 77
78 **The usage scenario** 78 **The usage scenario**
79 79
80 There are two ways to use names of databases obtained with this tool in Galaxy's version on snpEff: 80 There are two ways to use names of databases obtained with this tool in Galaxy's version on snpEff:
81 81
82 #. Use **SnpEff download** tool. It will download the database to the history and you will be able to use it in **SnpEff eff** tool using *Downloaded snpEff database in your history* option of the **Genome source** parameter. 82 #. Use **SnpEff download** tool. It will download the database to the history and you will be able to use it in **SnpEff eff** tool using *Downloaded snpEff database in your history* option of the **Genome source** parameter.
83 #. Use *Download on demand* option of the **SnpEff eff** tool (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation. 83 #. Use *Download on demand* option of the **SnpEff eff** tool (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation.
84 84
85 @snpeff_in_galaxy_info@ 85 @snpeff_in_galaxy_info@
86 @external_documentation@ 86 @external_documentation@
87 ]]></help> 87 ]]></help>
88 <expand macro="citations" /> 88 <expand macro="citations" />