| Previous changeset 25:ca337cce3888 (2022-10-14) Next changeset 27:03ed9524dcd1 (2023-01-15) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739 |
|
modified:
pangolin.xml |
| b |
| diff -r ca337cce3888 -r 007ffbb11881 pangolin.xml --- a/pangolin.xml Fri Oct 14 23:50:44 2022 +0000 +++ b/pangolin.xml Sun Jan 15 10:34:09 2023 +0000 |
| [ |
| @@ -1,8 +1,8 @@ <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01"> <description>Phylogenetic Assignment of Outbreak Lineages</description> <macros> - <token name="@TOOL_VERSION@">4.1.2</token> - <token name="@PANGOLIN_DATA_VERSION@">1.12</token> + <token name="@TOOL_VERSION@">4.1.3</token> + <token name="@PANGOLIN_DATA_VERSION@">1.17</token> <token name="@CONSTELLATIONS_VERSION@">0.1.10</token> <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token> <!-- a regex describing the scorpio versions that this wrapper version @@ -73,14 +73,14 @@ <requirement type="package" version="0.3.17">scorpio</requirement> <requirement type="package" version="@PANGOLIN_DATA_VERSION@">pangolin-data</requirement> <requirement type="package" version="@CONSTELLATIONS_VERSION@">constellations</requirement> - <requirement type="package" version="0.5.6">usher</requirement> + <requirement type="package" version="0.6.2">usher</requirement> <requirement type="package" version="1.1.0">gofasta</requirement> <requirement type="package" version="426">ucsc-fatovcf</requirement> <requirement type="package" version="2.24">minimap2</requirement> <!-- 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="0.23.0">csvtk</requirement> + <requirement type="package" version="0.25.0">csvtk</requirement> <requirement type="package" version="3.4">grep</requirement> </requirements> <version_command><![CDATA[pangolin --version]]></version_command> @@ -196,7 +196,7 @@ <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" /> <conditional name="engine"> <param argument="--analysis-mode" type="select" label="Analysis mode" - help="The analysis engine to use for lineage assignment. UShER is considered more accurate, but pangoLEARN is faster"> + help="The analysis engine to use for lineage assignment. UShER is considered more accurate; pangoLEARN typically requires more memory, but might be faster in some cases."> <option value="usher">UShER</option> <option value="pangolearn">pangoLEARN</option> </param> @@ -262,14 +262,13 @@ </data> </outputs> <tests> + <!-- Test only the default UShER mode for now since the + pangolearn random forest model uses too much memory + see https://github.com/cov-lineages/pangolin/issues/395 <test expect_num_outputs="1"> <param name="input1" value="test1.fasta"/> <conditional name="engine"> - <!-- Test only the default UShER mode for now since the - pangolearn random forest model uses too much memory - see https://github.com/cov-lineages/pangolin/issues/395 <param name="analysis_mode" value="pangolearn" /> - --> <conditional name="pangolin_data"> <param name="source" value="default" /> </conditional> @@ -282,21 +281,23 @@ </assert_contents> </output> </test> + --> <test expect_num_outputs="1"> <param name="input1" value="test1.fasta"/> <conditional name="engine"> <conditional name="pangolin_data"> - <param name="source" value="download" /> + <param name="source" value="default" /> </conditional> </conditional> <output name="output1" ftype="tabular"> <assert_contents> - <has_text_matching expression="B\.1\.1.*\t\d\.\d\t*PUSHER" /> + <has_text_matching expression="B\.1\.1.*\t\d\.\d+\t*PUSHER" /> <has_text text="pass" /> <has_n_lines n="1" /> </assert_contents> </output> </test> + <!-- test download and alignment options --> <test expect_num_outputs="2"> <param name="input1" value="test1.fasta" /> <conditional name="engine"> |