Mercurial > repos > iuc > data_manager_metaphlan_database_downloader
changeset 0:169b08c9713c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
author | iuc |
---|---|
date | Mon, 19 Apr 2021 20:54:06 +0000 |
parents | |
children | 9c43baa60906 |
files | data_manager/data_manager_metaphlan_download.py data_manager/data_manager_metaphlan_download.xml data_manager_conf.xml tool-data/metaphlan_database.loc.sample tool_data_table_conf.xml.sample |
diffstat | 5 files changed, 213 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_metaphlan_download.py Mon Apr 19 20:54:06 2021 +0000 @@ -0,0 +1,146 @@ +#!/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_metaphlan_db(data_tables, index, table_name, target_dp): + """Download MetaPhlAn database + + 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 + index: version + table_name: name of the table + target_dp: directory to put copy or link to the data file + + """ + db_dp = target_dp / Path(index) + cmd = "metaphlan --install --index %s --bowtie2db %s" % (index, db_dp) + subprocess.check_call(cmd, shell=True) + add_data_table_entry( + data_tables, + table_name, + dict( + dbkey=index, + value='%s-%s' % (index, date.today().strftime("%d%m%Y")), + name="MetaPhlAn clade-specific marker genes (%s)" % index, + path=str(db_dp))) + + +if __name__ == "__main__": + print("Starting...") + + # Read command line + parser = argparse.ArgumentParser(description='Download and build MetaPhlan database') + parser.add_argument('--index', help="Version of the database") + parser.add_argument('--json', help="Path to JSON file") + 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, "metaphlan_database") + + # Fetch data from specified data sources + print("Download and build database") + download_metaphlan_db( + data_tables, + args.index, + "metaphlan_database", + target_dp) + + # Write output JSON + print("Outputting JSON") + with open(json_fp, 'w') as fh: + json.dump(data_tables, fh, sort_keys=True) + print("Done.")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_metaphlan_download.xml Mon Apr 19 20:54:06 2021 +0000 @@ -0,0 +1,36 @@ +<tool id="data_manager_metaphlan_download" name="Download and build MetaPhlAn database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01"> + <description></description> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">metaphlan</requirement> + </requirements> + <macros> + <token name="@TOOL_VERSION@">3.0.7</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <command><![CDATA[ +python '$__tool_directory__/data_manager_metaphlan_download.py' + --index '$index' + --json '$out_file' + ]]></command> + <inputs> + <param name="index" type="select" label="Version"> + <option value="mpa_v30_CHOCOPhlAn_201901" selected="true">mpa_v30_CHOCOPhlAn_201901</option> + </param> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" label="${tool.name}"/> + </outputs> + <tests> + </tests> + <help><![CDATA[ +This tool downloads and builds the MetaPhlAn databases. + ]]></help> + <citations> + <citation type="doi">1101/2020.11.19.388223</citation> + <yield /> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Mon Apr 19 20:54:06 2021 +0000 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_metaphlan_download.xml" id="data_manager_metaphlan_download" > + <data_table name="metaphlan_database"> <!-- 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}">metaphlan/data/${dbkey}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/metaphlan/data/${dbkey}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metaphlan_database.loc.sample Mon Apr 19 20:54:06 2021 +0000 @@ -0,0 +1,4 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Apr 19 20:54:06 2021 +0000 @@ -0,0 +1,6 @@ +<tables> + <table name="metaphlan_database" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool-data/metaphlan_database.loc" /> + </table> +</tables>