Mercurial > repos > iuc > snpeff
diff snpEff_macros.xml @ 12:5a29ab10dba6 draft
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 | 479c4f2f4826 |
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--- a/snpEff_macros.xml Tue Mar 27 14:56:29 2018 -0400 +++ b/snpEff_macros.xml Thu Mar 29 20:39:49 2018 -0400 @@ -13,7 +13,7 @@ snpEff -version ]]></version_command> </xml> - <token name="@wrapper_version@">4.3.1t</token> + <token name="@wrapper_version@">4.3+T</token> <token name="@snpeff_version@">SnpEff4.3</token> <token name="@snpeff_database_url@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token> <token name="@java_options@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token> @@ -36,7 +36,7 @@ **Pre-cached databases** -Many standard (e.g., human, mouse, *Drosophila*) databases are likely pre-cached within a given Galaxy instance. You should be able to see them listed in **Genome** drop-down of **SbpEff eff** tool. +Many standard (e.g., human, mouse, *Drosophila*) databases are likely pre-cached within a given Galaxy instance. You should be able to see them listed in **Genome** drop-down of **SbpEff eff** tool. In you *do not see them* keep reading... @@ -48,17 +48,17 @@ #. Use **SnpEff download** tool to download the database. #. Finally, use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter. -Alternatively, you can specify the name of the database directly in **SnpEff eff** using the *Download on demand* option (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation. +Alternatively, you can specify the name of the database directly in **SnpEff eff** using the *Download on demand* option (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation. **Create your own database** In cases when you are dealing with bacterial or viral (or, frankly, any other) genomes it may be easier to create database yourself. For this you need: - #. Download Genbank record corresponding to your genome of interest from from NCBI. - #. Use **SnpEff build** to create the database. + #. Download Genbank record corresponding to your genome of interest from NCBI. + #. Use **SnpEff build** to create the database. #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter). -Creating custom database has one benefit. The **SnpEff build** tool normally produces two outputs: (1) a SnpEff database and (2) FASTA file containing sequences from the Genbank file. If you are performing your experiment from the beginning by mapping reads against a genome and finding variants before annotating them with SnpEff you can use **this FASTA file** as a reference to map your reads against. This will guarantee that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors. +Creating custom database has one benefit. The **SnpEff build** tool normally produces two outputs: (1) a SnpEff database and (2) FASTA file containing sequences from the Genbank file. If you are performing your experiment from the beginning by mapping reads against a genome and finding variants before annotating them with SnpEff you can use **this FASTA file** as a reference to map your reads against. This will guarantee that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors. </token> @@ -70,4 +70,4 @@ <yield /> </citations> </xml> -</macros> \ No newline at end of file +</macros>