Mercurial > repos > iuc > customize_metaphlan_database
changeset 11:a755466eb47c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
| author | iuc |
|---|---|
| date | Mon, 29 Jul 2024 07:14:38 +0000 |
| parents | 254cb00a578f |
| children | |
| files | customize_metaphlan_database.xml macros.xml test-data/SRS014464-Anterior_nares.fastq.gz test-data/test_database_versioned.loc test-data/test_database_versioned.loc.test tool_data_table_conf.xml.test |
| diffstat | 6 files changed, 20 insertions(+), 11 deletions(-) [+] |
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--- a/customize_metaphlan_database.xml Tue Apr 30 09:08:54 2024 +0000 +++ b/customize_metaphlan_database.xml Mon Jul 29 07:14:38 2024 +0000 @@ -5,7 +5,7 @@ </macros> <expand macro="edam_ontology"/> <expand macro="requirements"> - <requirement type="package" version="1.3">seqtk</requirement> + <requirement type="package" version="1.4">seqtk</requirement> </expand> <version_command>metaphlan -v</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/macros.xml Tue Apr 30 09:08:54 2024 +0000 +++ b/macros.xml Mon Jul 29 07:14:38 2024 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">4.0.6</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@TOOL_VERSION@">4.1.1</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.05</token> <!-- Metaphlan DB compatible with this version of Metaphlan v4 introduced single genome level bins (SGB) and the index syntax differs from previous versions --> @@ -23,4 +23,9 @@ <citation type="doi">10.7554/eLife.65088</citation> </citations> </xml> + + <xml name="subsample_common"> + <param argument="--mapping_subsampling" type="boolean" truevalue="--mapping_subsampling" falsevalue="" label="Subsampling on the mapping results" help="instead of on the reads"/> + <param argument="--subsampling_seed" type="integer" optional="true" label="Subsampling seed" help="No value: random"/> + </xml> </macros>
--- a/test-data/test_database_versioned.loc Tue Apr 30 09:08:54 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -# Tab separated with 5 columns: -# - value (Galaxy records this in the Galaxy DB) -# - name (Galaxy shows this in the UI) -# - value (Galaxy records this in the Galaxy DB) -# - path (folder name containing the Kraken DB) -# - db version (whether it is SGB of Metaphlan v4 or not) -test-db-20210409 "Test Database" test-db ${__HERE__}/test-db SGB
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_database_versioned.loc.test Mon Jul 29 07:14:38 2024 +0000 @@ -0,0 +1,11 @@ +# Tab separated with 5 columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - dbkey +# - path (folder name containing the Kraken DB) +# - db version (whether it is SGB of Metaphlan v4 or not) +test-db-20210409 "Test Database" test-db ${__HERE__}/test-db SGB +# the TOY DB should be called in tests with the hidden test parameter enables this will make Metaphlan +# download the data to the JWD +mpa_vJan21_TOY_CHOCOPhlAnSGB mpa_vJan21_TOY_CHOCOPhlAnSGB mpa_vJan21_TOY_CHOCOPhlAnSGB_202103 ./ SGB +# mpa_vJun23_CHOCOPhlAnSGB_202403 mpa_vJun23_CHOCOPhlAnSGB_202403 mpa_vJun23_CHOCOPhlAnSGB_202403 ${__HERE__}/mpa_vJun23_CHOCOPhlAnSGB_202403/ SGB
--- a/tool_data_table_conf.xml.test Tue Apr 30 09:08:54 2024 +0000 +++ b/tool_data_table_conf.xml.test Mon Jul 29 07:14:38 2024 +0000 @@ -2,6 +2,6 @@ <tables> <table name="metaphlan_database_versioned" comment_char="#"> <columns>value, name, dbkey, path, db_version</columns> - <file path="${__HERE__}/test-data/test_database_versioned.loc"/> + <file path="${__HERE__}/test-data/test_database_versioned.loc.test"/> </table> </tables>