| Previous changeset 15:36912871ccdc (2021-12-13) Next changeset 17:5f8727ff21e7 (2022-01-31) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b" |
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modified:
pangolin.xml |
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| diff -r 36912871ccdc -r ca0d8cf80567 pangolin.xml --- a/pangolin.xml Mon Dec 13 11:02:29 2021 +0000 +++ b/pangolin.xml Wed Dec 15 19:39:45 2021 +0000 |
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| @@ -1,10 +1,11 @@ -<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01"> +<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01"> <description>Phylogenetic Assignment of Outbreak Lineages</description> <macros> <token name="@TOOL_VERSION@">3.1.17</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement> + <requirement type="package" version="0.3.16">scorpio</requirement> <requirement type="package" version="0.23.0">csvtk</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -45,7 +46,7 @@ <param name="include_header" type="boolean" label="Include header line in output file" truevalue="true" falsevalue="false" /> <conditional name="db"> - <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database"> + <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database. While 'Download latest from web' is recommended, if errors occur see the warning in the main help text below."> <option value="download">Download latest from web</option> <option value="builtin">Use database from Galaxy server</option> <option value="default">Use default database built in to pangolin (not recommended)</option> @@ -162,6 +163,11 @@ model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the default model rapidly becomes out of date. +.. class:: warningmark + + The "Download latest from web" updates the pangolin database but not the pangolin (and scorpio) software. If + the database format changes this can cause the pangolin job and the tool to fail. The solution to this kind of + failure is to update the pangolin tool installed in the Galaxy server. ]]></help> <citations> <citation type="doi">10.1093/ve/veab064</citation> |