Mercurial > repos > iuc > snpeff

annotate snpeff_get_chr_names.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
children
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ebe9fd7e5bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 280d5247becaa9a70db9c5c4a2f1fc50d302838a
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1 <tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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2 <description>list chromosome names/lengths</description>
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3 <macros>
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4 <import>snpEff_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <expand macro="requirement">
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8 <requirement type="package" version="5.0.1">gawk</requirement>
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9 </expand>
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10 </requirements>
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11 <expand macro="stdio" />
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12 <expand macro="version_command" />
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13 <command detect_errors="exit_code"><![CDATA[
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14 snpEff @JAVA_OPTIONS@ dump
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15 #if $snpDb.genomeSrc == 'cached':
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16 -dataDir ${snpDb.genomeVersion.fields.path}
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17 $snpDb.genomeVersion
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18 #elif $snpDb.genomeSrc == 'history':
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19 -dataDir '${snpDb.snpeff_db.extra_files_path}'
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20 '${snpDb.snpeff_db.metadata.genome_version}'
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21 #elif $snpDb.genomeSrc == 'custom':
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22 -dataDir '${snpDb.snpeff_db.extra_files_path}'
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23 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}'
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24 '${snpDb.snpeff_db.metadata.genome_version}'
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25 #else
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26 -dataDir "\$PWD/temp"
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27 -download
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28 '$snpDb.genome_version'
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29 #end if
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30 | awk '/# Chromosomes/{y=1;next}y' | grep "#" | grep -E "[0-9]" | awk 'BEGIN {err=1;} {c=$0;sub(/^[^a-zA-Z0-9_]+/, "", c) && err=0; sub(/[^a-zA-Z0-9_]+/, "\t", c) && err=0; sub(/[^0-9]*$/, "", c) && err=0; print c } END {exit err}' > '$chr_names'
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31 ]]></command>
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32 <inputs>
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33 <conditional name="snpDb">
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34 <param name="genomeSrc" type="select" label="Genome source">
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35 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well -->
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36 <option value="cached">Locally installed snpEff database</option>
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37 <option value="history">Downloaded snpEff database in your history</option>
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38 <option value="named">Download on demand</option>
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39 <option value="custom">Custom snpEff database in your history</option>
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40 </param>
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41 <when value="cached">
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42 <param name="genomeVersion" type="select" label="Genome">
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43 <help>This can only be used on built-in databases manually configured by your galaxy admin.</help>
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44 <options from_data_table="snpeffv_genomedb">
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45 <filter type="regexp" column="1" value="@COMPATIBLE_DB_VERSIONS_REGEX@" />
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46 <filter type="unique_value" column="2" />
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47 </options>
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48 </param>
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49 </when>
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50 <when value="history">
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51 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
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52 <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help>
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53 <validator type="expression" message="This version of SnpEff will only work with @COMPATIBLE_DB_VERSIONS_STRING@ genome databases">value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@</validator>
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54 </param>
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55 </when>
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56 <when value="named">
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57 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)">
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58 <help>The list of available databases can be obtained with 'SnpEff databases' tool. If the database name is not found, locate a database here and download it in your history.</help>
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59 <validator type="regex" message="A genome version name is required">\S+</validator>
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60 </param>
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61 </when>
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62 <when value="custom">
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63 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
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64 <help>This can only be used on databases in your history that were created using the snpEff build tool.</help>
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65 <validator type="expression" message="This version of SnpEff will only work with @COMPATIBLE_DB_VERSIONS_STRING@ genome databases">value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@</validator>
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66 </param>
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67 </when>
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68 </conditional>
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69 </inputs>
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70 <outputs>
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71 <data format="tabular" name="chr_names" label="Chromosome names and sizes"/>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <conditional name="snpDb">
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76 <param name="genomeSrc" value="cached"/>
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77 <param name="genomeVersion" value="ebola_zaire"/>
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78 </conditional>
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79 <output name="chr_names">
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80 <assert_contents>
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81 <has_text text="KJ660346" />
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82 <has_text text="18959" />
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83 </assert_contents>
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84 </output>
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85 </test>
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86 <test expect_failure="True">
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87 <conditional name="snpDb">
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88 <param name="genomeSrc" value="named"/>
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89 <param name="genome_version" value="should_not_match"/>
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90 </conditional>
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94
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95 **What it does**
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96
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97 This tool outputs a tab-delimited file of chromosome names and their lengths, as they are in the selected genome/SnpEff database. The output can be used to validate and rename chromosomes in VCF files in order to annotate its records.
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98
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99 Note, make sure that the genome you select from the snpEff database precisely matches the one used in your analysis. As a cursory check, you can use the chromosome lengths in this output to match those in your reference, however the lengths can match, but the version may still differ.
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100
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101 Known issue: this strategy will not work if more than 1 chromosome in the same genome has the same length.
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102
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103 -------
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104
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105 .. class:: infomark
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106
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107 **The usage scenario**
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108
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109 Suppose you want to use snpEff to annotate a VCF file that was generated using an mouse reference with a different chromosome naming convention than in the snpEff database. To do this you can:
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110
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111 #. Use `SnpEff databases` to find the precise genome name for mouse data (e.g. "mm10") as it appears in the snpEff database.
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112 #. List the chromosome names using this tool. Either select a built-in genome, one in your history, or select "Download on demand" and enter the genome version obtained in the previous step (which only actually downloads if snpEff doesn't already have it).
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113 #. Check that the chromosomes in the SnpEff database are the same as the reference you used (e.g. as a cursory check, ensure the chromosome lengths reported from the SnpEff database match those of your reference).
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114 #. Edit your vcf file to replace the chromosome names with the ones the SnpEff database uses.
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115 #. Use **SnpEff eff** and supply the edited VCF file.
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116
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117 ]]></help>
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118 <expand macro="citations" />
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119 </tool>