Mercurial > repos > ufz > virsorter_build_database
changeset 0:863ba94fb6e4 draft
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_virsorter commit fdde667342e69dd11ef98029e0d6d3376d0d95c7
author | ufz |
---|---|
date | Sun, 23 Jun 2024 16:48:31 +0000 |
parents | |
children | ad63dbb3493a |
files | data_manager/virsorter_datamanager.xml data_manager_conf.xml tool-data/virsorter.loc.sample tool_data_table_conf.xml.sample |
diffstat | 4 files changed, 90 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/virsorter_datamanager.xml Sun Jun 23 16:48:31 2024 +0000 @@ -0,0 +1,60 @@ +<?xml version="1.0"?> +<tool id="virsorter_build_database" name="virsorter" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <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="@PROFILE@">22.01</token> + <!-- zenodo ID and therebut 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 + --> + <token name="@VIRSORTER_DB_VERSION@">0.4</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">virsorter</requirement> + <requirement type="package" version="1.21.4">wget</requirement> + <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 && + cp '$dmjson' '$out_file' + ]]></command> + <configfiles> + <configfile name="dmjson"><![CDATA[ +{ + "data_tables":{ + "virsorter":[ + { + "path":"db", + "name":"Version @VIRSORTER_DB_VERSION@", + "virsorter_version":"@TOOL_VERSION@", + "value":"@VIRSORTER_DB_VERSION@" + } + ] + } +}]]> + </configfile> + </configfiles> + <inputs/> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <tests> + <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> + </tests> + <help><![CDATA[ +Download and extract virsorter database version @VIRSORTER_DB_VERSION@ from zenodo (https://zenodo.org/records/10594875) + ]]></help> + <citations> + <citation type="doi">10.1186/s40168-020-00990-y</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Sun Jun 23 16:48:31 2024 +0000 @@ -0,0 +1,19 @@ +<data_managers> + <data_manager tool_file="data_manager/virsorter_datamanager.xml" id="virsorter_build_database"> + <data_table name="virsorter"> + <output> + <column name="value"/> + <column name="name"/> + <column name="virsorter_version"/> + <column name="path" output_ref="out_file"> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">virsorter/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/virsorter/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/virsorter.loc.sample Sun Jun 23 16:48:31 2024 +0000 @@ -0,0 +1,3 @@ +# Format: +# value name virsorter_version path +# value must be the version of the database, e.g. 0.4, needs to be a number \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Jun 23 16:48:31 2024 +0000 @@ -0,0 +1,8 @@ +<tables> + <!-- virsorter reference data --> + <table name="virsorter" comment_char="#"> + <!-- value should be the version (https://zenodo.org/records/4297575) --> + <columns>value, name, virsorter_version, path</columns> + <file path="tool-data/virsorter.loc" /> + </table> +</tables> \ No newline at end of file