Mercurial > repos > iuc > pangolin
changeset 31:12ed89df38ed draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin commit 6f18af1157e861524c024f3a3c9255ac0a41729a
| author | iuc |
|---|---|
| date | Mon, 16 Feb 2026 10:45:50 +0000 |
| parents | 5f736365108b |
| children | |
| files | pangolin.xml |
| diffstat | 1 files changed, 11 insertions(+), 77 deletions(-) [+] |
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--- a/pangolin.xml Mon Nov 17 12:56:52 2025 +0000 +++ b/pangolin.xml Mon Feb 16 10:45:50 2026 +0000 @@ -1,8 +1,8 @@ -<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy2" profile="21.09"> +<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy3" profile="24.2"> <description>Phylogenetic Assignment of Outbreak Lineages</description> <macros> <token name="@TOOL_VERSION@">4.3.4</token> - <token name="@PANGOLIN_DATA_VERSION@">1.26</token> + <token name="@PANGOLIN_DATA_VERSION@">1.37</token> <token name="@CONSTELLATIONS_VERSION@">0.1.12</token> <!-- a regex describing the pangolin-data versions that this wrapper version is backwards-compatible with; can be used with the min_pangolin_version @@ -49,8 +49,9 @@ versions become available. Also, please check for updated dependencies when updating the wrapper for other reasons. --> <requirement type="package" version="0.3.19">scorpio</requirement> - <requirement type="package" version="1.36">pangolin-data</requirement> - <requirement type="package" version="0.1.12">constellations</requirement> + <!-- Important: keep the following two versions tokenized since the tokens are reused in the inputs section! --> + <requirement type="package" version="@PANGOLIN_DATA_VERSION@">pangolin-data</requirement> + <requirement type="package" version="@CONSTELLATIONS_VERSION@">constellations</requirement> <requirement type="package" version="0.6.6">usher</requirement> <requirement type="package" version="1.2.3">gofasta</requirement> <requirement type="package" version="482">ucsc-fatovcf</requirement> @@ -58,7 +59,7 @@ <!-- wrapper-specific requirements to turn pangolin's native comma-separated output into tab-separated one and to truncate pangolin's all-versions output. --> - <requirement type="package" version="0.35.0">csvtk</requirement> + <requirement type="package" version="0.36.0">csvtk</requirement> <requirement type="package" version="3.12">grep</requirement> </requirements> <version_command><![CDATA[pangolin --version]]></version_command> @@ -68,47 +69,9 @@ ## for at least one of pangolin-data and constellations we need to ## provide a non-conda env version through a datadir mkdir datadir && - #if str($engine.pangolin_data.source) == 'download' or str($constellations.source) == 'download': - ## If "download latest from web" got requested for any data component, - ## we can make use of pangolin --update-data to do the job for us. - ## However, this would download updated versions of *all* data - ## packages into our datadir, while the user may have asked for - ## just a specific one. To avoid this, we set up a fake package - ## with very high version number in the datadir to prevent - ## unwanted component updates. After updating the rest of the - ## data, we remove the fake package again. - #if str($engine.pangolin_data.source) != 'download': - mkdir datadir/pangolin_data && - echo '__version__ = "999"' > datadir/pangolin_data/__init__.py && - #end if - #if str($constellations.source) != 'download': - mkdir datadir/constellations && - ## constellations versions start with a 'v'! - echo '__version__ = "v999"' > datadir/constellations/__init__.py && - #end if - ## download updated packages discarding stdout because we - ## output final package versions separately below and because - ## it would contain our fake package versions - pangolin --update-data --datadir datadir 2&> /dev/null && - #if str($engine.pangolin_data.source) != 'download': - rm -r datadir/pangolin_data && - #end if - #if str($constellations.source) != 'download': - rm -r datadir/constellations && - #end if - #end if - #if str($engine.analysis_mode) == 'usher' and str($engine.pangolin_data.source) == 'download': - #if $engine.pangolin_data.use_assignment_cache: - ## We need to download also the latest UShER assignment cache data. - ## Since v4.1 pangolin's - ## --add-assignment-cache/--use-assignment-cache options respect - ## --datadir so we can use them directly. - pangolin --datadir datadir --add-assignment-cache && - #end if - #end if ## Handle data components to be taken from data tables ## The folder structure pointed to by the data tables can be used - ## as is except that cannot symlink the folders themselves since + ## as is except that we cannot symlink the folders themselves since ## pangolin inspects them using os.walk with the default ## `followlinks=False`. ## Since data table versions of data packages can be older than @@ -148,9 +111,7 @@ #end if --analysis-mode $engine.analysis_mode #if str($engine.analysis_mode) == 'usher': - #if str($engine.pangolin_data.source) == 'download': - $engine.pangolin_data.use_assignment_cache - #else if str($engine.pangolin_data.source) == 'cached': + #if str($engine.pangolin_data.source) == 'cached': #if $engine.pangolin_data.assignment_cache_release: --use-assignment-cache #end if @@ -183,7 +144,6 @@ <param name="source" type="select" label="Version of pangolin-data to use"> <option value="default">Use pangolin-data version (v@PANGOLIN_DATA_VERSION@) shipped with this version of the tool</option> <option value="cached">Use specific pangolin-data version cached on this Galaxy server</option> - <option value="download">Download latest available pangolin-data version from web</option> </param> <when value="default" /> <when value="cached"> @@ -200,10 +160,6 @@ </param> <expand macro="cached_usher_assignment_cache" /> </when> - <when value="download"> - <param argument="--use-assignment-cache" type="boolean" truevalue="--use-assignment-cache" falsevalue="" label="Download and use also latest UShER assignment cache?" - help="Get the latest UShER assignment cache from the pangolin-assignment online repository and use it to speed up UShER lineage assignment. Note: Downloading the cached assignments will only pay off for large numbers of input samples." /> - </when> </conditional> </when> <when value="pangolearn"> @@ -232,7 +188,6 @@ <param name="source" type="select" label="Version of constellations to use"> <option value="default">Use constellations version (v@CONSTELLATIONS_VERSION@) shipped with this version of the tool</option> <option value="cached">Use specific constellations version cached on this Galaxy server</option> - <option value="download">Download latest available constellations version from web</option> </param> <when value="default" /> <when value="cached"> @@ -248,7 +203,6 @@ </options> </param> </when> - <when value="download" /> </conditional> <param argument="--alignment" type="boolean" truevalue="--alignment" falsevalue="" label="Output multiple sequence alignment of input sequences" /> <param argument="--max-ambig" type="float" value="0.3" min="0" max="1" label="Maximum proportion of Ns allowed" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" /> @@ -310,7 +264,7 @@ </assert_contents> </output> </test> - <!-- test download and alignment options --> + <!-- test alignment options --> <test expect_num_outputs="2"> <param name="input1" value="test1.fasta" /> <conditional name="engine"> @@ -320,10 +274,10 @@ <param name="analysis_mode" value="pangolearn" /> --> <conditional name="pangolin_data"> - <param name="source" value="download" /> + <param name="source" value="default" /> </conditional> </conditional> - <param name="alignment" value="--alignment" /> + <param name="alignment" value="true" /> <output name="output1" ftype="tabular"> <assert_contents> <has_text_matching expression="B\.1\.1\t\d\.\d" /> @@ -420,26 +374,6 @@ of the shipped versions, which can be useful to reproduce results obtained earlier with previous versions of pangolin. -Finally, you have the option to *download the latest version* of each data -package at job runtime. - -.. class:: warningmark - - You can use this option as a workaround to get the most up-to-date lineage - assignments even before the next Galaxy tool update (or before an admin - installs new cached data versions on your server), but be aware of the - following limitations: - -1. Using latest downloaded data package versions renders results hard to - reproduce (e.g. rerunning a corresponding job will cause also a fresh - data download, which may yield different data versions as in the intial - run). - -2. Downloaded latest versions of the data packages may be incompatible - with the *pangolin* and *scorpio* version run by the tool, which can - result in failing tool runs, but occasionally also in harder to diagnose - lineage assignment issues. - .. class:: infomark The exact combination of pangolin, inference engine (UShER/pangoLEARN),