| Previous changeset 7:7bb8726be37c (2021-07-20) Next changeset 9:3a43c3982401 (2021-08-29) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 5a3f70ab430c70b260dd6e0f5b6c53aed2ca5520" |
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modified:
pangolin.xml |
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| diff -r 7bb8726be37c -r 3a656a4a43ed pangolin.xml --- a/pangolin.xml Tue Jul 20 12:23:51 2021 +0000 +++ b/pangolin.xml Fri Aug 13 19:53:03 2021 +0000 |
| [ |
| @@ -1,7 +1,7 @@ <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01"> <description>Phylogenetic Assignment of Outbreak Lineages</description> <macros> - <token name="@TOOL_VERSION@">3.1.7</token> + <token name="@TOOL_VERSION@">3.1.11</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement> @@ -9,7 +9,7 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ #if str($db.source) == "download" - python '$__tool_directory__/fetch_latest_pangolearn.py' --max_retries=$db.max_retries --timeout=$db.timeout && + pangolin --update-data --datadir datadir && #else if str($db.source) == "builtin" ln -s $db.db_release.fields.path datadir && #end if @@ -51,8 +51,9 @@ <option value="default">Use default database built in to pangolin (not recommended)</option> </param> <when value="download"> - <param name="max_retries" label="Max download retries" help="How many times to retry downloading the pangoLEARN database" type="integer" value="5" /> - <param name="timeout" label="Download timeout" help="How many seconds to wait when downloading the pangoLEARN database" type="float" value="60.0" /> + <!-- these are currently not supported by the pangolin downloader --> + <!-- <param name="max_retries" label="Max download retries" help="How many times to retry downloading the pangoLEARN database" type="integer" value="5" /> --> + <!-- <param name="timeout" label="Download timeout" help="How many seconds to wait when downloading the pangoLEARN database" type="float" value="60.0" /> --> </when> <when value="builtin"> <param name="db_release" label="pangoLEARN release" type="select"> @@ -173,17 +174,6 @@ </assert_contents> </output> </test> - <test expect_failure="true"> - <param name="input1" value="test1.fasta" /> - <conditional name="db"> - <param name="source" value="download" /> - <param name="timeout" value="0.00001" /> - <param name="max_retries" value="1" /> - </conditional> - <assert_stderr> - <has_text text="timed out" /> - </assert_stderr> - </test> </tests> <help><![CDATA[ @@ -201,14 +191,6 @@ ]]></help> <citations> - <citation type="bibtex"> - @misc{githubpangolin, - author = {O'Toole, Áine}, - year = {2020}, - title = {pangolin}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/cov-lineages/pangolin}, - }</citation> + <citation type="doi">10.1093/ve/veab064</citation> </citations> </tool> |