Mercurial > repos > iuc > snpeff

annotate snpEff_macros.xml @ 33:94653948fdb9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5
author iuc
date Sat, 04 Oct 2025 17:00:46 +0000
parents ebe9fd7e5bd1
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1 <macros>
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2 <!-- TOKENS TO BE UPDATED -->
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3 <token name="@TOOL_VERSION@">5.2</token>
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4 <token name="@VERSION_SUFFIX@">1</token>
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5 <token name="@SNPEFF_VERSION@">SnpEff5.2</token>
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6 <!-- SnpEff versions are usually backwards compatible with a few older database versions.
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7 The authoritative place to look up the compatibility scheme is DATABASE_COMPATIBLE_VERSIONS in Config.java of the upstream code.
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8 Currently this would be:
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9 https://github.com/pcingola/SnpEff/blob/master/src/main/java/org/snpeff/snpEffect/Config.java#L37-L52
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11 The three following tokens define the list of compatible DB versions for the wrapper (for input validation), a human-readable string (for parameter help/labels) and a regex of the same versions (for filtering of data table records). -->
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12 <token name="@COMPATIBLE_DB_VERSIONS@">['SnpEff5.0', 'SnpEff5.1', 'SnpEff5.2']</token>
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13 <token name="@COMPATIBLE_DB_VERSIONS_STRING@">SnpEff 5.0 - 5.2</token>
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14 <token name="@COMPATIBLE_DB_VERSIONS_REGEX@"><![CDATA[^SnpEff5\.[0-2]$]]></token>
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15 <!-- End of TOKENS TO BE UPDATED -->
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17 <xml name="requirement">
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18 <requirement type="package" version="@TOOL_VERSION@">snpeff</requirement>
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19 <yield/>
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20 </xml>
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21 <xml name="stdio">
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22 <stdio>
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23 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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24 <exit_code range="1:" level="fatal" description="Error" />
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25 </stdio>
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26 </xml>
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27 <xml name="version_command">
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28 <version_command><![CDATA[
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29 snpEff -version
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30 ]]></version_command>
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31 </xml>
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32 <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
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33 <xml name="ref_select">
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34 <conditional name="reference_source">
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35 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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36 <option value="cached">Locally cached</option>
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37 <option value="history">History</option>
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38 </param>
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39 <when value="cached">
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40 <param name="ref_file" type="select" label="Select reference genome">
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41 <options from_data_table="fasta_indexes"/>
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42 </param>
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43 </when>
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44 <when value="history">
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45 <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Genome in FASTA format" help="This dataset is required for generating SnpEff database. See help section below."/>
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46 </when>
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47 </conditional>
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48 </xml>
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49 <token name="@EXTERNAL_DOCUMENTATION@">
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52 -------
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54 To learn more about snpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html
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55 </token>
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56 <token name="@SNPEFF_IN_GALAXY_INFO@">
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58 -------
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60 .. class:: warningmark
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62 **Using SnpEff in Galaxy: A few points to remember**
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64 SnpEff relies on specially formatted databases to generate annotations. It will not work without them. There are several ways in which these databases can be obtained.
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66 **Pre-cached databases**
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67
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68 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 **SnpEff eff** tool.
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70 In you *do not see them* keep reading...
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72 **Download pre-built databases**
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74 SnpEff project generates large numbers of pre-build databases. To obtain and use them follow these steps:
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76 #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need.
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77 #. Use **SnpEff download** tool to download the database.
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78 #. 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.
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80 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.
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82 **Create your own database**
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84 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:
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86 #. Download Genbank record corresponding to your genome of interest from NCBI or use annotations in GFF format accompanied by the corresponding genome in FASTA format.
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87 #. Use **SnpEff build** to create the database.
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88 #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter).
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89
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90 Creating custom database has one major advantage. It guaranteess that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors.
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91
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92 </token>
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93
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94
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95
0
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96 <xml name="citations">
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97 <citations>
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98 <citation type="doi">10.4161/fly.19695</citation>
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99 <yield />
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100 </citations>
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101 </xml>
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102 </macros>