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comparison 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
comparison
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32:ebe9fd7e5bd1 33:94653948fdb9
40 </param> 40 </param>
41 <when value="cached"> 41 <when value="cached">
42 <param name="genomeVersion" type="select" label="Genome"> 42 <param name="genomeVersion" type="select" label="Genome">
43 <help>This can only be used on built-in databases manually configured by your galaxy admin.</help> 43 <help>This can only be used on built-in databases manually configured by your galaxy admin.</help>
44 <options from_data_table="snpeffv_genomedb"> 44 <options from_data_table="snpeffv_genomedb">
45 <filter type="static_value" name="SNPEFF_VERSION" value="@SNPEFF_VERSION@" column="1"/> 45 <filter type="regexp" column="1" value="@COMPATIBLE_DB_VERSIONS_REGEX@" />
46 <filter type="unique_value" column="2" /> 46 <filter type="unique_value" column="2" />
47 </options> 47 </options>
48 </param> 48 </param>
49 </when> 49 </when>
50 <when value="history"> 50 <when value="history">
51 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> 51 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
52 <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help> 52 <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help>
53 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator> 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>
54 </param> 54 </param>
55 </when> 55 </when>
56 <when value="named"> 56 <when value="named">
57 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)"> 57 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)">
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> 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>
60 </param> 60 </param>
61 </when> 61 </when>
62 <when value="custom"> 62 <when value="custom">
63 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> 63 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
64 <help>This can only be used on databases in your history that were created using the snpEff build tool.</help> 64 <help>This can only be used on databases in your history that were created using the snpEff build tool.</help>
65 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator> 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>
66 </param> 66 </param>
67 </when> 67 </when>
68 </conditional> 68 </conditional>
69 </inputs> 69 </inputs>
70 <outputs> 70 <outputs>
71 <data format="tabular" name="chr_names" label="Chromosome names and sizes"/> 71 <data format="tabular" name="chr_names" label="Chromosome names and sizes"/>
72 </outputs> 72 </outputs>
73 <tests> 73 <tests>
74 <test> 74 <test>
75 <param name="genomeSrc" value="named"/> 75 <conditional name="snpDb">
76 <param name="genome_version" value="Bacillus_subtilis_subsp_subtilis_str_168"/> 76 <param name="genomeSrc" value="cached"/>
77 <param name="genomeVersion" value="ebola_zaire"/>
78 </conditional>
77 <output name="chr_names"> 79 <output name="chr_names">
78 <assert_contents> 80 <assert_contents>
79 <has_text text="Chromosome" /> 81 <has_text text="KJ660346" />
80 <has_text text="4215606" /> 82 <has_text text="18959" />
81 </assert_contents> 83 </assert_contents>
82 </output> 84 </output>
83 </test> 85 </test>
84 <test expect_failure="True"> 86 <test expect_failure="True">
85 <param name="genomeSrc" value="named"/> 87 <conditional name="snpDb">
86 <param name="genome_version" value="should_not_match"/> 88 <param name="genomeSrc" value="named"/>
89 <param name="genome_version" value="should_not_match"/>
90 </conditional>
87 </test> 91 </test>
88 </tests> 92 </tests>
89 <help><![CDATA[ 93 <help><![CDATA[
90 94
91 **What it does** 95 **What it does**