| Next changeset 1:3756ac7a625b (2024-09-20) |
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Commit message:
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_checkv commit 625d1e8699c69e5ee3caef0cc5c883a9d9e6ac91 |
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added:
data_manager/checkv_datamanager.xml data_manager_conf.xml tool-data/genomad.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 4bd77968fe29 data_manager/checkv_datamanager.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/checkv_datamanager.xml Mon Sep 16 09:53:52 2024 +0000 |
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| @@ -0,0 +1,63 @@ +<tool id="checkv_build_database" name="CheckV" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>database builder</description> + <macros> + <token name="@TOOL_VERSION@">1.0.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + </macros> + <requirements> + <!-- DM only needs diamon (which comes with checkv) --> + <requirement type="package" version="@TOOL_VERSION@">checkv</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + set -eo pipefail; + wget https://portal.nersc.gov/CheckV/checkv-db-v${version}.tar.gz && + tar -zxvf checkv-db-v${version}.tar.gz && + cd checkv-db-v${version}/genome_db/ && + diamond makedb --in checkv_reps.faa --db checkv_reps && + cd - && + mv checkv-db-v${version} checkv-db && + cp '$dmjson' '$out_file' + ]]></command> + <configfiles> + <configfile name="dmjson"><![CDATA[ +{ + "data_tables":{ + "checkv":[ + { + "path":"", + "name":"Version $version", + "version":"$version", + "value":"$version" + } + ] + } +}]]> + </configfile> + </configfiles> + <inputs> + <param name="version" type="select" multiple="false" label="Database Version"> + <option value="1.5">1.5</option> + </param> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <tests> + <!-- <test expect_num_outputs="1"> + <param name="version" value="1.5" /> + <output name="out_file"> + <assert_contents> + <has_text text='"value":"1.5"'/> + <has_text text='"name":"Version 1.5"'/> + </assert_contents> + </output> + </test> --> + </tests> + <help><![CDATA[ +Download and extract CheckV reference data from https://portal.nersc.gov/CheckV/ + ]]></help> + <citations> + <citation type="doi">10.1038/s41587-020-00774-7</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 4bd77968fe29 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Mon Sep 16 09:53:52 2024 +0000 |
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| @@ -0,0 +1,19 @@ +<data_managers> + <data_manager tool_file="data_manager/checkv_datamanager.xml" id="checkv_build_database"> + <data_table name="checkv"> + <output> + <column name="value"/> + <column name="name"/> + <column name="version"/> + <column name="path" output_ref="out_file"> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">checkv/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/checkv/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> |
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| diff -r 000000000000 -r 4bd77968fe29 tool-data/genomad.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/genomad.loc.sample Mon Sep 16 09:53:52 2024 +0000 |
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| @@ -0,0 +1,3 @@ +# Format: +# value name path +# value must be the version of the database, e.g. 1.7, needs to be a number \ No newline at end of file |
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| diff -r 000000000000 -r 4bd77968fe29 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Sep 16 09:53:52 2024 +0000 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- checkv reference data --> + <table name="checkv" comment_char="#"> + <columns>value, name, version, path</columns> + <file path="tool-data/checkv.loc" /> + </table> +</tables> |