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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4" |
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added:
data_manager/data_manager_semibin.py data_manager/data_manager_semibin.xml data_manager_conf.xml test-data/gtdb.loc tool-data/gtdb.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 676915c44e1e data_manager/data_manager_semibin.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_semibin.py Fri Oct 14 21:32:55 2022 +0000 |
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| @@ -0,0 +1,153 @@ +#!/usr/bin/env python +# +# Data manager for reference data for the MetaPhlAn Galaxy tools +import argparse +import json +import subprocess +from datetime import date +from pathlib import Path + + +# Utility functions for interacting with Galaxy JSON +def read_input_json(json_fp): + """Read the JSON supplied from the data manager tool + + Returns a tuple (param_dict,extra_files_path) + + 'param_dict' is an arbitrary dictionary of parameters + input into the tool; 'extra_files_path' is the path + to a directory where output files must be put for the + receiving data manager to pick them up. + + NB the directory pointed to by 'extra_files_path' + doesn't exist initially, it is the job of the script + to create it if necessary. + + """ + with open(json_fp) as fh: + params = json.load(fh) + return (params['param_dict'], + Path(params['output_data'][0]['extra_files_path'])) + + +# Utility functions for creating data table dictionaries +# +# Example usage: +# >>> d = create_data_tables_dict() +# >>> add_data_table(d,'my_data') +# >>> add_data_table_entry(dict(dbkey='hg19',value='human')) +# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse')) +# >>> print(json.dumps(d)) +def create_data_tables_dict(): + """Return a dictionary for storing data table information + + Returns a dictionary that can be used with 'add_data_table' + and 'add_data_table_entry' to store information about a + data table. It can be converted to JSON to be sent back to + the data manager. + + """ + d = { + 'data_tables': {} + } + return d + + +def add_data_table(d, table): + """Add a data table to the data tables dictionary + + Creates a placeholder for a data table called 'table'. + + """ + d['data_tables'][table] = [] + + +def add_data_table_entry(d, table, entry): + """Add an entry to a data table + + Appends an entry to the data table 'table'. 'entry' + should be a dictionary where the keys are the names of + columns in the data table. + + Raises an exception if the named data table doesn't + exist. + + """ + try: + d['data_tables'][table].append(entry) + except KeyError: + raise Exception("add_data_table_entry: no table '%s'" % table) + + +def download_gtdb(data_tables, table_name, target_dp, test=False): + """Download GTDB + + Creates references to the specified file(s) on the Galaxy + server in the appropriate data table (determined from the + file extension). + + The 'data_tables' dictionary should have been created using + the 'create_data_tables_dict' and 'add_data_table' functions. + + Arguments: + data_tables: a dictionary containing the data table info + table_name: name of the table + target_dp: directory to put copy or link to the data file + + """ + db_dp = target_dp + if not test: + cmd = "SemiBin download_GTDB --reference-db-data-dir %s" % (db_dp) + subprocess.check_call(cmd, shell=True) + dbkey = 'gtdb' + name = "GTDB reference genome generated by MMseqs2 used in SemiBin" + else: + dbkey = 'test' + name = "Test" + empty_fp = db_dp / Path("empty") + empty_fp.touch() + add_data_table_entry( + data_tables, + table_name, + dict( + dbkey=dbkey, + value='%s' % (date.today().strftime("%d%m%Y")), + name=name, + path=str(db_dp))) + + +if __name__ == "__main__": + print("Starting...") + + # Read command line + parser = argparse.ArgumentParser(description='Download reference genomes (GTDB)') + parser.add_argument('--json', help="Path to JSON file") + parser.add_argument('--test', action='store_true', help="Test") + args = parser.parse_args() + print("args : %s" % args) + + # Read the input JSON + json_fp = Path(args.json) + params, target_dp = read_input_json(json_fp) + + # Make the target directory + print("Making %s" % target_dp) + target_dp.mkdir(parents=True, exist_ok=True) + + # Set up data tables dictionary + data_tables = create_data_tables_dict() + add_data_table(data_tables, "gtdb") + + # Fetch data from specified data sources + print("Download and build database") + download_gtdb( + data_tables, + "gtdb", + target_dp, + args.test) + + # Write output JSON + print("Outputting JSON") + with open(json_fp, 'w') as fh: + json.dump(data_tables, fh, sort_keys=True) + print("Done.") |
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| diff -r 000000000000 -r 676915c44e1e data_manager/data_manager_semibin.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_semibin.xml Fri Oct 14 21:32:55 2022 +0000 |
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| @@ -0,0 +1,39 @@ +<tool id="data_manager_semibin" name="Download reference genomes (GTDB) for SemiBin" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description></description> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">semibin</requirement> + </requirements> + <macros> + <token name="@TOOL_VERSION@">1.1.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> + </macros> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/data_manager_semibin.py' + --json '$out_file' + $type + ]]></command> + <inputs> + <param name="type" type="hidden" value="" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="type" value="--test" /> + <output name="out_file"> + <assert_contents> + <has_text text="test"/> + <has_text text="Test"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +This tool downloads reference genomes (GTDB) for SemiBin + ]]></help> + <citations> + <citation type="doi">10.1038/s41467-022-29843-y</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 676915c44e1e data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Fri Oct 14 21:32:55 2022 +0000 |
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| @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_semibin.xml" id="data_manager_semibin" > + <data_table name="gtdb"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="dbkey" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="path" output_ref="out_file" > + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">semibin/data/${dbkey}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/semibin/data/${dbkey}</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 676915c44e1e test-data/gtdb.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtdb.loc Fri Oct 14 21:32:55 2022 +0000 |
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| @@ -0,0 +1,3 @@ +#file has this format (white space characters are TAB characters) +#dbkey description name /path/to/data +test-date description test /path/to/data \ No newline at end of file |
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| diff -r 000000000000 -r 676915c44e1e tool-data/gtdb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gtdb.loc.sample Fri Oct 14 21:32:55 2022 +0000 |
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| @@ -0,0 +1,2 @@ +#file has this format (white space characters are TAB characters) +#dbkey description name /path/to/data |
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| diff -r 000000000000 -r 676915c44e1e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Oct 14 21:32:55 2022 +0000 |
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| @@ -0,0 +1,6 @@ +<tables> + <table name="gtdb" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool-data/gtdb.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 676915c44e1e tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Oct 14 21:32:55 2022 +0000 |
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| @@ -0,0 +1,6 @@ +<tables> + <table name="gtdb" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="${__HERE__}/test-data/gtdb.loc" /> + </table> +</tables> \ No newline at end of file |