| Previous changeset 0:863ba94fb6e4 (2024-06-23) Next changeset 2:c456ae8354f2 (2024-12-18) |
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Commit message:
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_virsorter commit c78bd5eafa3d9450305cc8b32ba9cf8c64c42ba7 |
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modified:
data_manager/virsorter_datamanager.xml |
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| diff -r 863ba94fb6e4 -r ad63dbb3493a data_manager/virsorter_datamanager.xml --- a/data_manager/virsorter_datamanager.xml Sun Jun 23 16:48:31 2024 +0000 +++ b/data_manager/virsorter_datamanager.xml Mon Nov 18 15:26:28 2024 +0000 |
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| @@ -3,9 +3,9 @@ <description>database builder</description> <macros> <token name="@TOOL_VERSION@">2.2.4</token> <!-- when updating make sure to double check the db version --> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">22.01</token> - <!-- zenodo ID and therebut the version of the reference data is hardcoded in the current version virsorter: + <!-- zenodo ID and the version of the reference data is hardcoded in the current version virsorter: https://github.com/jiarong/VirSorter2/blob/c0dcac53f3373244bf1bd552a7c2104d53802df7/virsorter/rules/setup.smk#L13 check and update the DB version when updating the VS version might also change/improve in the future https://github.com/jiarong/VirSorter2/issues/205#issuecomment-2184184977 @@ -18,7 +18,12 @@ <requirement type="package" version="2.7.0">pulp</requirement> <!-- needs to be pinned, because the old-ish snakemake used in vs2 struggles with https://github.com/snakemake/snakemake/issues/2607 --> </requirements> <command detect_errors="exit_code"><![CDATA[ - virsorter setup -d db -j \${GALAXY_SLOTS:-1} --skip-deps-install && + mkdir -p '$out_file.extra_files_path'/db && + #if $test == "true" + touch '$out_file.extra_files_path'/db/test && + #else + virsorter setup -d '$out_file.extra_files_path'/db -j \${GALAXY_SLOTS:-1} --skip-deps-install && + #end if cp '$dmjson' '$out_file' ]]></command> <configfiles> @@ -37,22 +42,34 @@ }]]> </configfile> </configfiles> - <inputs/> + <inputs> + <param name="test" type="hidden"/> + </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> <tests> <test expect_num_outputs="1"> + <param name="test" value="true"/> + <output name="out_file"> + <assert_contents> + <has_text text='"value":"@VIRSORTER_DB_VERSION@"'/> + <has_text text='"name":"Version @VIRSORTER_DB_VERSION@"'/> + </assert_contents> + </output> + </test> + <!-- 10GB test data seem to be to much for CI. but this test should be executed locally for updates + <test expect_num_outputs="1"> <output name="out_file"> <assert_contents> <has_text text='"value":"@VIRSORTER_DB_VERSION@"'/> <has_text text='"name":"Version @VIRSORTER_DB_VERSION@"'/> </assert_contents> </output> - </test> + </test> --> </tests> <help><![CDATA[ -Download and extract virsorter database version @VIRSORTER_DB_VERSION@ from zenodo (https://zenodo.org/records/10594875) +Download and extract virsorter database version @VIRSORTER_DB_VERSION@ from zenodo (https://zenodo.org/records/4269607) ]]></help> <citations> <citation type="doi">10.1186/s40168-020-00990-y</citation> |