| Previous changeset 1:592ef3959907 (2023-04-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709 |
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modified:
data_manager/data_manager_build_amrfinderplus.py data_manager/data_manager_build_amrfinderplus.xml data_manager/macro.xml data_manager_conf.xml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/amrfinderplus_versioned.loc.test tool-data/amrfinderplus_versioned.loc.sample |
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removed:
test-data/amrfinderplus.loc.test test-data/amrfinderplus_test_data_manager_2.json tool-data/amrfinderplus.loc.sample |
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| diff -r 592ef3959907 -r a5921c09b7b7 data_manager/data_manager_build_amrfinderplus.py --- a/data_manager/data_manager_build_amrfinderplus.py Sun Apr 16 08:29:18 2023 +0000 +++ b/data_manager/data_manager_build_amrfinderplus.py Thu May 30 13:06:37 2024 +0000 |
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| @@ -15,7 +15,7 @@ """ def __init__(self, - amrfinderplus_database="amrfinderplus_database", + amrfinderplus_database="amrfinderplus_versioned_database", db_name="amrfinderplus-db", amrfinderplus_version="latest", date_version=None): @@ -50,6 +50,7 @@ f"-{self._amrfinderplus_date_version}" data_info = dict(value=amrfinderplus_value, name=amrfinderplus_name, + db_version=self._amrfinderplus_version, path=self._db_name) self.amrfinderplus_table_list["data_tables"][self.data_table_name] = [data_info] return self.amrfinderplus_table_list @@ -110,8 +111,6 @@ """ self.amrfinderplus_db_path = f'{self._output_dir}/{self._db_name}' os.makedirs(self.amrfinderplus_db_path) - if self._amrfinderplus_version == 'latest': - self.get_amrfinderplus_version() amrfinderplus_ftp_path = f"ftp://{self._login}:" \ f"{self._password}@{self._ncbi_ftp_url}/" \ |
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| diff -r 592ef3959907 -r a5921c09b7b7 data_manager/data_manager_build_amrfinderplus.xml --- a/data_manager/data_manager_build_amrfinderplus.xml Sun Apr 16 08:29:18 2023 +0000 +++ b/data_manager/data_manager_build_amrfinderplus.xml Thu May 30 13:06:37 2024 +0000 |
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| @@ -1,62 +1,28 @@ <tool id="data_manager_build_amrfinderplus" name="amrfinderplus_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> - <description>AMRfinderplus database builder</description> + <description>AMRFinderPlus database builder</description> <macros> <import>macro.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"> <![CDATA[ - python '$__tool_directory__/data_manager_build_amrfinderplus.py' - '$output_file' - --db_version '$database_list.database_version_select' - #if $database_list.database_version_select != 'latest': - --db_date '$database_list.database_date_select' - #end if - $test_data_manager +python '$__tool_directory__/data_manager_build_amrfinderplus.py' + '$output_file' + --db_version '$database_list.database_version_select' + #if $database_list.database_version_select != 'latest': + --db_date '$database_list.database_date_select' + #end if + $test_data_manager ]]></command> <inputs> <conditional name="database_list"> <param name="database_version_select" type="select" label="Database version"> - <option value="latest" selected="true">Latest available version</option> - <option value="3.10">V3.10</option> - <option value="3.9">V3.9</option> - <option value="3.8">V3.8</option> - <option value="3.6">V3.6</option> + <option value="3.12">V3.12</option> </param> - <when value="latest"> - </when> - <when value="3.10"> + <when value="3.12"> <param name="database_date_select" type="select" label="Date version"> - <option value="2022-10-11.2" selected="true">2022-10-11.2</option> - <option value="2022-08-09.1">2022-08-09.1</option> - <option value="2022-05-26.1">2022-05-26.1</option> - <option value="2022-04-04.1">2022-04-04.1</option> - <option value="2021-12-21.1">2021-12-21.1</option> - <option value="2021-09-30.1">2021-09-30.1</option> - <option value="2021-09-30.1">2021-08-11.1</option> - <option value="2021-09-30.1">2021-06-01.1</option> - <option value="2021-09-30.1">2021-03-01.1</option> - </param> - </when> - <when value="3.9"> - <param name="database_date_select" type="select" label="Date version"> - <option value="2020-11-09.1" selected="true">2020-11-09.1</option> - <option value="2020-12-17.1">2020-12-17.1</option> - </param> - </when> - <when value="3.8"> - <param name="database_date_select" type="select" label="Date version"> - <option value="2020-09-30.1" selected="true">2020-09-30.1</option> - <option value="2020-09-22.2">2020-09-22.2</option> - <option value="2020-07-16.2">2020-07-16.2</option> - <option value="2020-06-11.1">2020-06-11.1</option> - <option value="2020-05-04.1">2020-05-04.1</option> - </param> - </when> - <when value="3.6"> - <param name="database_date_select" type="select" label="Date version"> - <option value="2020-01-22.1" selected="true">2020-01-22.1</option> - <option value="2020-03-20.1">2020-03-20.1</option> + <option value="2024-05-02.2">2024-05-02.2</option> + <option value="2024-01-31.1">2024-01-31.1</option> </param> </when> </conditional> @@ -73,24 +39,31 @@ <assert_contents> <has_n_lines n="1"/> <has_text text="{"data_tables""/> - <has_text text="amrfinderplus_database"/> + <has_text text="amrfinderplus_versioned_database"/> + <has_text text='"db_version": "3.12"'/> </assert_contents> </output> </test> - <!-- Test_2 DB 3.2 --> + <!-- Test_2 DB 3.12 2024-01-31.1 --> <test expect_num_outputs="1"> <param name="test_data_manager" value="--test"/> <conditional name="database_list"> - <param name="database_version_select" value="3.6"/> - <param name="database_date_select" value="2020-03-20.1"/> + <param name="database_version_select" value="3.12"/> + <param name="database_date_select" value="2024-01-31.1"/> </conditional> - <output name="output_file" value="amrfinderplus_test_data_manager_2.json"/> + <output name="output_file"> + <assert_contents> + <has_n_lines n="1"/> + <has_text text="{"data_tables""/> + <has_text text="amrfinderplus_versioned_database"/> + <has_text text='"name": "V3.12-2024-01-31.1"'/> + <has_text text='"db_version": "3.12"'/> + </assert_contents> + </output> </test> - - </tests> <help><![CDATA[ - Download amrfinderplus database from the NCBI server +Download AMRFinderPlus database from the NCBI server ]]></help> <citations> <citation type="doi">10.1038/s41598-021-91456-0</citation> |
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| diff -r 592ef3959907 -r a5921c09b7b7 data_manager/macro.xml --- a/data_manager/macro.xml Sun Apr 16 08:29:18 2023 +0000 +++ b/data_manager/macro.xml Thu May 30 13:06:37 2024 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">3.10.45</token> + <token name="@TOOL_VERSION@">3.12.8</token> <token name="@PYTHON_VERSION@">3.10.6</token> <token name="@PANDAS@">1.5.1</token> <token name="@VERSION_SUFFIX@">0</token> |
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| diff -r 592ef3959907 -r a5921c09b7b7 data_manager_conf.xml --- a/data_manager_conf.xml Sun Apr 16 08:29:18 2023 +0000 +++ b/data_manager_conf.xml Thu May 30 13:06:37 2024 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <data_managers> <data_manager tool_file="data_manager/data_manager_build_amrfinderplus.xml" id="data_manager_build_amrfinderplus"> - <data_table name="amrfinderplus_database"> + <data_table name="amrfinderplus_versioned_database"> <output> <column name="value" /> <column name="name" /> |
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| diff -r 592ef3959907 -r a5921c09b7b7 test-data/amrfinderplus.loc.test --- a/test-data/amrfinderplus.loc.test Sun Apr 16 08:29:18 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 amrfinderplus database -# -# the columns are: -# value, name, path -# -# for example -amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 amrfinderplus-db -amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 amrfinderplus-db |
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| diff -r 592ef3959907 -r a5921c09b7b7 test-data/amrfinderplus_test_data_manager_2.json --- a/test-data/amrfinderplus_test_data_manager_2.json Sun Apr 16 08:29:18 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"amrfinderplus_database": [{"name": "V3.6-2020-03-20.1", "path": "amrfinderplus-db", "value": "amrfinderplus_V3.6_2020-03-20.1"}]}} \ No newline at end of file |
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| diff -r 592ef3959907 -r a5921c09b7b7 test-data/amrfinderplus_versioned.loc.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus_versioned.loc.test Thu May 30 13:06:37 2024 +0000 |
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| @@ -0,0 +1,10 @@ +# this is a tab separated file describing the location of amrfinderplus database +# +# the columns are: +# value, name, db_version, path +# +# for example +amrfinderplus_V3.12_2024-05-02.2 V3.12-2024-05-02.2 3.12 amrfinderplus-db +amrfinderplus_V3.12_2024-01-31.1 V3.12-2024-01-31.1 3.12 amrfinderplus-db +amrfinderplus_V3.12_2024-05-02.2 V3.12-2024-05-02.2 3.12 /private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp3d_yq23a/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.12_2024-05-02.2 +amrfinderplus_V3.12_2024-01-31.1 V3.12-2024-01-31.1 3.12 /private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp3d_yq23a/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.12_2024-01-31.1 |
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| diff -r 592ef3959907 -r a5921c09b7b7 tool-data/amrfinderplus.loc.sample --- a/tool-data/amrfinderplus.loc.sample Sun Apr 16 08:29:18 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -# this is a tab separated file describing the location of amrfinderplus database -# -# the columns are: -# value, name, path -# -# for example -#amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 amrfinderplus-db |
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| diff -r 592ef3959907 -r a5921c09b7b7 tool-data/amrfinderplus_versioned.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/amrfinderplus_versioned.loc.sample Thu May 30 13:06:37 2024 +0000 |
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| @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of amrfinderplus database +# +# the columns are: +# value, name, db_version, path +# +# for example +#amrfinderplus_V3.12_2024-05-02.2 V3.12-2024-05-02.2 3.12 amrfinderplus-db |
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| diff -r 592ef3959907 -r a5921c09b7b7 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sun Apr 16 08:29:18 2023 +0000 +++ b/tool_data_table_conf.xml.sample Thu May 30 13:06:37 2024 +0000 |
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| @@ -1,7 +1,7 @@ <tables> <!-- Locations of amrfinderplus database in the required format --> - <table name="amrfinderplus_database" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/amrfinderplus.loc" /> + <table name="amrfinderplus_versioned_database" comment_char="#"> + <columns>value, name, db_version, path</columns> + <file path="tool-data/amrfinderplus_versioned.loc" /> </table> </tables> \ No newline at end of file |
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| diff -r 592ef3959907 -r a5921c09b7b7 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Sun Apr 16 08:29:18 2023 +0000 +++ b/tool_data_table_conf.xml.test Thu May 30 13:06:37 2024 +0000 |
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| @@ -1,7 +1,7 @@ <tables> <!-- Locations of amrfinderplus database in the required format --> - <table name="amrfinderplus_database" comment_char="#"> - <columns>value, name, path</columns> - <file path="${__HERE__}/test-data/amrfinderplus.loc.test"/> + <table name="amrfinderplus_versioned_database" comment_char="#"> + <columns>value, name, db_version, path</columns> + <file path="${__HERE__}/test-data/amrfinderplus_versioned.loc.test"/> </table> </tables> |