| Next changeset 1:3f68072f2da6 (2024-11-18) |
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Commit message:
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_vibrant commit 652d6d214d2de01b29badbb1fad8648d6fd6153b |
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added:
data_manager/vibrant_datamanager.xml data_manager_conf.xml tool-data/vibrant.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 200343b50d46 data_manager/vibrant_datamanager.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/vibrant_datamanager.xml Mon Sep 16 09:52:54 2024 +0000 |
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| @@ -0,0 +1,55 @@ +<tool id="vibrant_build_database" name="vibrant" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>database builder</description> + <macros> + <token name="@TOOL_VERSION@">1.2.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + </macros> + <xrefs> + <xref type="bio.tools">VIBRANT</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">vibrant</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + set -eo pipefail; + download-db.sh vibrant_db && + cp '$dmjson' '$out_file' + ]]></command> + <configfiles> + <configfile name="dmjson"><![CDATA[ +{ + "data_tables":{ + "vibrant":[ + { + "path":"vibrant_db", + "name":"Version @TOOL_VERSION@", + "version":"@TOOL_VERSION@", + "value":"@TOOL_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":"@TOOL_VERSION@"'/> + <has_text text='"name":"Version @TOOL_VERSION@"'/> + </assert_contents> + </output> + </test> --> + </tests> + <help><![CDATA[ +Download and vibrant reference data using https://raw.githubusercontent.com/AnantharamanLab/VIBRANT/master/databases/VIBRANT_setup.py + ]]></help> + <citations> + <citation type="doi">10.1186/s40168-020-00867-0</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 200343b50d46 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Mon Sep 16 09:52:54 2024 +0000 |
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| @@ -0,0 +1,19 @@ +<data_managers> + <data_manager tool_file="data_manager/vibrant_datamanager.xml" id="vibrant_build_database"> + <data_table name="vibrant"> + <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}">vibrant_databases/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/vibrant_databases/${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 200343b50d46 tool-data/vibrant.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/vibrant.loc.sample Mon Sep 16 09:52:54 2024 +0000 |
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| @@ -0,0 +1,7 @@ +# data for vibrant can be downloaded using download-db.sh +# - value needs to be a unique identifier (maybe date) +# - name what is shown to the user +# - version store the vibrant version +# - path +# Format: +# value name version path \ No newline at end of file |
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| diff -r 000000000000 -r 200343b50d46 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 09:52:54 2024 +0000 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- vibrant reference data --> + <table name="vibrant" comment_char="#"> + <columns>value, name, version, path</columns> + <file path="tool-data/vibrant.loc" /> + </table> +</tables> |