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comparison pangolin.xml @ 29:f0fc9c4f00fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin commit 89a03f607cc5f9862ebc6f6e1f3111c9dbc6ccdf
author iuc
date Mon, 27 Oct 2025 09:30:25 +0000
parents 3ccccf6c08cd
children 5f736365108b
comparison
equal deleted inserted replaced
28:3ccccf6c08cd 29:f0fc9c4f00fe
1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01"> 1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy2" profile="21.09">
2 <description>Phylogenetic Assignment of Outbreak Lineages</description> 2 <description>Phylogenetic Assignment of Outbreak Lineages</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">4.3</token> 4 <token name="@TOOL_VERSION@">4.3.2</token>
5 <token name="@PANGOLIN_DATA_VERSION@">1.21</token> 5 <token name="@PANGOLIN_DATA_VERSION@">1.26</token>
6 <token name="@CONSTELLATIONS_VERSION@">0.1.12</token> 6 <token name="@CONSTELLATIONS_VERSION@">0.1.12</token>
7 <!-- a regex describing the pangolin-data versions that this wrapper version 7 <!-- a regex describing the pangolin-data versions that this wrapper version
8 is backwards-compatible with; can be used with the min_pangolin_version 8 is backwards-compatible with; can be used with the min_pangolin_version
9 column of the pangolin_data and pangolin_assignment data table to offer 9 column of the pangolin_data and pangolin_assignment data table to offer
10 only compatible versions of that data. --> 10 only compatible versions of that data. -->
29 <filter type="param_value" ref="release" column="0" /> 29 <filter type="param_value" ref="release" column="0" />
30 </options> 30 </options>
31 </param> 31 </param>
32 </xml> 32 </xml>
33 </macros> 33 </macros>
34 <xrefs>
35 <xref type="bio.tools">pangolin_cov-lineages</xref>
36 </xrefs>
34 <requirements> 37 <requirements>
35 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement> 38 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
36 <!-- Pin also the versions of all core dependencies - the ones 39 <!-- Pin also the versions of all core dependencies - the ones
37 reported with the all-versions option of pangolin and which have a 40 reported with the all-versions option of pangolin and which have a
38 direct impact on the lineage assignment process - to the versions 41 direct impact on the lineage assignment process - to the versions
43 the all-versions option as long as the user doesn't update the data 46 the all-versions option as long as the user doesn't update the data
44 dependencies. 47 dependencies.
45 Wrapper updates are **explicitly encouraged** when new dependency 48 Wrapper updates are **explicitly encouraged** when new dependency
46 versions become available. Also, please check for updated dependencies 49 versions become available. Also, please check for updated dependencies
47 when updating the wrapper for other reasons. --> 50 when updating the wrapper for other reasons. -->
48 <requirement type="package" version="0.3.17">scorpio</requirement> 51 <requirement type="package" version="0.3.19">scorpio</requirement>
49 <requirement type="package" version="@PANGOLIN_DATA_VERSION@">pangolin-data</requirement> 52 <requirement type="package" version="1.35">pangolin-data</requirement>
50 <requirement type="package" version="@CONSTELLATIONS_VERSION@">constellations</requirement> 53 <requirement type="package" version="0.1.12">constellations</requirement>
51 <requirement type="package" version="0.6.2">usher</requirement> 54 <requirement type="package" version="0.6.6">usher</requirement>
52 <requirement type="package" version="1.2.0">gofasta</requirement> 55 <requirement type="package" version="1.2.3">gofasta</requirement>
53 <requirement type="package" version="448">ucsc-fatovcf</requirement> 56 <requirement type="package" version="482">ucsc-fatovcf</requirement>
54 <requirement type="package" version="2.26">minimap2</requirement> 57 <requirement type="package" version="2.30">minimap2</requirement>
55 <!-- wrapper-specific requirements to turn pangolin's native 58 <!-- wrapper-specific requirements to turn pangolin's native
56 comma-separated output into tab-separated one and to truncate 59 comma-separated output into tab-separated one and to truncate
57 pangolin's all-versions output. --> 60 pangolin's all-versions output. -->
58 <requirement type="package" version="0.26.0">csvtk</requirement> 61 <requirement type="package" version="0.35.0">csvtk</requirement>
59 <requirement type="package" version="3.11">grep</requirement> 62 <requirement type="package" version="3.12">grep</requirement>
60 </requirements> 63 </requirements>
61 <version_command><![CDATA[pangolin --version]]></version_command> 64 <version_command><![CDATA[pangolin --version]]></version_command>
62 <command detect_errors="exit_code"><![CDATA[ 65 <command detect_errors="exit_code"><![CDATA[
63 ## Prepare a pangolin datadir if required: 66 ## Prepare a pangolin datadir if required:
64 #if str($engine.pangolin_data.source) != 'default' or str($constellations.source) != 'default': 67 #if str($engine.pangolin_data.source) != 'default' or str($constellations.source) != 'default':