Mercurial > repos > card > rgi
changeset 4:ce852ee2c394 draft
planemo upload for repository https://github.com/arpcard/rgi commit 78185f967f4c08824f0b118214adcecc14495f3e
| author | card |
|---|---|
| date | Wed, 31 Aug 2022 01:14:48 +0000 |
| parents | bfbfc24c5af2 |
| children | 84bd24ac33fd |
| files | data_managers/data_manager_conf.xml data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml rgi.xml |
| diffstat | 3 files changed, 11 insertions(+), 5 deletions(-) [+] |
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--- a/data_managers/data_manager_conf.xml Fri Nov 20 18:57:39 2020 +0000 +++ b/data_managers/data_manager_conf.xml Wed Aug 31 01:14:48 2022 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager_rgi_build_db/data_manager/rgi_database_builder.xml" id="rgi_database_builder" version="1.1.0"> + <data_manager tool_file="data_manager_rgi_build_db/data_manager/rgi_database_builder.xml" id="rgi_database_builder" version="1.2.0"> <!-- Defines a Data Table to be modified --> <data_table name="rgi_databases"> <!-- Handle the output of the Data Manager Tool -->
--- a/data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml Fri Nov 20 18:57:39 2020 +0000 +++ b/data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml Wed Aug 31 01:14:48 2022 +0000 @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<tool id="rgi_database_builder" name="RGI Database Builder" tool_type="manage_data" version="1.1.0"> +<tool id="rgi_database_builder" name="RGI Database Builder" tool_type="manage_data" version="1.2.0"> <description>Download and build the CARD database for RGI</description> <requirements> - <requirement type="package" version="5.1.1">rgi</requirement> + <requirement type="package" version="5.2.1">rgi</requirement> </requirements> <stdio> <exit_code description="Error" level="fatal" range="1:" />
--- a/rgi.xml Fri Nov 20 18:57:39 2020 +0000 +++ b/rgi.xml Wed Aug 31 01:14:48 2022 +0000 @@ -1,12 +1,18 @@ -<tool id="rgi" name="Resistance Gene Identifier (RGI)" version="5.1.1"> +<tool id="rgi" name="Resistance Gene Identifier (RGI)" version="5.2.1"> <description>This tool predicts resistome(s) from protein or nucleotide data based on homology and SNP models.</description> <requirements> - <requirement type="package" version="5.1.1">rgi</requirement> + <requirement type="package" version="5.2.1">rgi</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command detect_errors="aggressive"><![CDATA[ +#if $db_opts.db_opts_selector == "default": + export DB_PATH='${__tool_data_path__}/rgi_databases/_default' && + export DATA_PATH="\$_GALAXY_JOB_TMP_DIR" && + mkdir -p "\$DB_PATH" && +#end if + #if $db_opts.db_opts_selector != "default": rgi load #if $db_opts.db_opts_selector == "local":