| Previous changeset 5:60cfd33bc2fb (2023-07-24) Next changeset 7:ed0f59ab5e61 (2023-08-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 3b2a82fa2ba8408609a72fefd18571223f080a6d |
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modified:
data_manager/plasmidfinder_fetch_database.xml data_manager_conf.xml test-data/plasmidfinder.loc.test tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
tool-data/plasmidfinder_database.loc.sample |
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removed:
tool-data/plasmidfinder_database.loc |
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| diff -r 60cfd33bc2fb -r 4e933a39094f data_manager/plasmidfinder_fetch_database.xml --- a/data_manager/plasmidfinder_fetch_database.xml Mon Jul 24 10:00:33 2023 +0000 +++ b/data_manager/plasmidfinder_fetch_database.xml Wed Aug 23 08:23:25 2023 +0000 |
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| @@ -9,7 +9,6 @@ python '$__tool_directory__/plasmidfinder_fetch_database.py' --db_version '$database_select' '$output_file' - && cat '$output_file' ]]></command> <inputs> <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)"> |
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| diff -r 60cfd33bc2fb -r 4e933a39094f data_manager_conf.xml --- a/data_manager_conf.xml Mon Jul 24 10:00:33 2023 +0000 +++ b/data_manager_conf.xml Wed Aug 23 08:23:25 2023 +0000 |
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| @@ -1,4 +1,3 @@ -<?xml version="1.0"?> <data_managers> <data_manager tool_file="data_manager/plasmidfinder_fetch_database.xml" id="plasmidfinder_fetch_database"> <data_table name="plasmidfinder_database"> @@ -9,9 +8,9 @@ <column name="path" output_ref="output_file"> <move type="directory" relativize_symlinks="True"> <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">plasmidfinder_database/${name}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">plasmidfinder-db/${name}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/plasmidfinder_database/${name}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/plasmidfinder-db/${name}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> |
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| diff -r 60cfd33bc2fb -r 4e933a39094f test-data/plasmidfinder.loc.test --- a/test-data/plasmidfinder.loc.test Mon Jul 24 10:00:33 2023 +0000 +++ b/test-data/plasmidfinder.loc.test Wed Aug 23 08:23:25 2023 +0000 |
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| @@ -1,9 +1,1 @@ -plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmptllq5k0r/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28 -plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmpnshbzr8f/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28 -plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmpgfqg6r8x/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28 -plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmpam2pha1m/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28 -plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmp_tzl62ye/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28 -plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmpu0batsz4/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28 -plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmp72f81ayd/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28 -plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmp73run5j6/galaxy-dev/tool-data/plasmidfinder_database/2.1_2019_08_28 -plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmpngljkg08/galaxy-dev/tool-data/plasmidfinder_database/2.1_2019_08_28 +plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 plasmidfinder-db |
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| diff -r 60cfd33bc2fb -r 4e933a39094f tool-data/plasmidfinder_database.loc --- a/tool-data/plasmidfinder_database.loc Mon Jul 24 10:00:33 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -# this is a tab separated file describing the location of plasmidfinder database -# The name was obtained by merging date of download and commit number -# the columns are: -# value, name, date, path -# -# for example -#plasmidfinder_9002e7282dd0_2022-12-20 9002e7282dd0_2022-12-20 2022-12-20 plasmidfinder-db -#plasmidfinder_1307168b1ce7_2022-12-20 2.1_2022-12-20 2022-12-20 plasmidfinder-db |
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| diff -r 60cfd33bc2fb -r 4e933a39094f tool-data/plasmidfinder_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder_database.loc.sample Wed Aug 23 08:23:25 2023 +0000 |
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| @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of plasmidfinder database +# The name was obtained by merging date of download and commit number +# the columns are: +# value, name, date, path +# +# for example +#plasmidfinder_9002e7282dd0_2022-12-20 9002e7282dd0_2022-12-20 2022-12-20 plasmidfinder-db +#plasmidfinder_1307168b1ce7_2022-12-20 2.1_2022-12-20 2022-12-20 plasmidfinder-db |
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| diff -r 60cfd33bc2fb -r 4e933a39094f tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Mon Jul 24 10:00:33 2023 +0000 +++ b/tool_data_table_conf.xml.sample Wed Aug 23 08:23:25 2023 +0000 |
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| @@ -3,6 +3,6 @@ <!-- Locations of plasmidfinder database in the required format --> <table name="plasmidfinder_database" comment_char="#"> <columns>value, name, date, path</columns> - <file path="tool-data/plasmidfinder.loc" /> + <file path="tool-data/plasmidfinder_database.loc.sample" /> </table> </tables> |
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| diff -r 60cfd33bc2fb -r 4e933a39094f tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Mon Jul 24 10:00:33 2023 +0000 +++ b/tool_data_table_conf.xml.test Wed Aug 23 08:23:25 2023 +0000 |
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| @@ -1,7 +1,7 @@ <tables> <!-- Locations of plasmidfinder database in the required format --> - <table name="plasmidfinder_database" comment_char="#"> - <columns>value, name, date, path</columns> + <table name="plasmidfinder_database" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, date, path</columns> <file path="${__HERE__}/test-data/plasmidfinder.loc.test"/> </table> </tables> |