| Previous changeset 20:14ae456b8cc5 (2022-05-03) Next changeset 22:a2099fb98cdb (2022-07-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 35c4813d132f69036addcc447cc6c4ec7da04d92" |
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modified:
pangolin.xml |
| b |
| diff -r 14ae456b8cc5 -r 81804a978fc0 pangolin.xml --- a/pangolin.xml Tue May 03 19:27:06 2022 +0000 +++ b/pangolin.xml Sat May 07 19:52:10 2022 +0000 |
| [ |
| @@ -1,16 +1,16 @@ -<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01"> +<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy2" profile="20.01"> <description>Phylogenetic Assignment of Outbreak Lineages</description> <macros> <token name="@TOOL_VERSION@">4.0.5</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement> - <requirement type="package" version="0.3.16">scorpio</requirement> + <requirement type="package" version="0.3.17">scorpio</requirement> <requirement type="package" version="0.23.0">csvtk</requirement> </requirements> <version_command><![CDATA[pangolin --version]]></version_command> <command detect_errors="exit_code"><![CDATA[ - #if $engine.use_assignment_cache and str($db.source) != "download": + #if $str($engine.analysis_mode) == 'usher' and $engine.use_assignment_cache and str($db.source) != "download": ## This is no good. Better to fail immediately instead of downloading a lot of data first. echo "Using the latest assignment cache requires downloading the latest version of pangolin-data." 1>&2; exit 1 #else: @@ -22,7 +22,7 @@ #else if str($db.source) == "builtin" ln -s $db.db_release.fields.path datadir && #end if - #if $engine.use_assignment_cache: + #if str($engine.analysis_mode) == 'usher' and $engine.use_assignment_cache: ## We need to install also the latest UShER assignment cache data. ## Pangolin has functionality to do so, but uses it incorrectly. ## We use the pangolin function to install into --datadir here, @@ -217,6 +217,16 @@ </assert_contents> </output> </test> + <!-- Test that use of latest assignment cache requires downloaded other data --> + <test expect_failure="true"> + <param name="input1" value="multiple_alignment.fasta.gz"/> + <conditional name="engine"> + <param name="use_assignment_cache" value="true" /> + </conditional> + <conditional name="db"> + <param name="source" value="default" /> + </conditional> + </test> <!-- test with extra expanded_lineage column --> <test expect_num_outputs="1"> <param name="input1" value="multiple_alignment.fasta.gz"/> |