| Next changeset 1:1316375a8cbb (2017-03-13) |
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Commit message:
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061 |
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added:
data_manager/data_manager_humann2_download.py data_manager/data_manager_humann2_download.xml data_manager_conf.xml tool-data/humann2_nucleotide_database.loc.sample tool-data/humann2_protein_database.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 048593e41359 data_manager/data_manager_humann2_download.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_humann2_download.py Sun Mar 12 14:33:34 2017 -0400 |
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| @@ -0,0 +1,177 @@ +#!/usr/bin/env python +# +# Data manager for reference data for the 'humann2' Galaxy tools +import datetime +import json +import optparse +import os +import subprocess +import sys + + +HUMANN2_REFERENCE_DATA = { + "full": "Full", + "DEMO": "Demo", + "uniref50_diamond": "Full UniRef50", + "uniref50_ec_filtered_diamond": "EC-filtered UniRef50", + "uniref50_GO_filtered_rapsearch2": "GO filtered UniRef50 for rapsearch2", + "uniref90_diamond": "Full UniRef50", + "uniref90_ec_filtered_diamond": "EC-filtered UniRef90", + "DEMO_diamond": "Demo" +} + + +# Utility functions for interacting with Galaxy JSON +def read_input_json(jsonfile): + """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. + + """ + params = json.loads(open(jsonfile).read()) + return (params['param_dict'], + 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 str(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 = {} + 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_humann2_db(data_tables, table_name, database, build, target_dir): + """Download HUMAnN2 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 + table_name: name of the table + database: database to download (chocophlan or uniref) + build: build of the database to download + target_dir: directory to put copy or link to the data file + + """ + value = "%s-%s-%s" % (database, build, datetime.date.today().isoformat()) + db_target_dir = os.path.join(target_dir, database) + build_target_dir = os.path.join(db_target_dir, build) + os.makedirs(build_target_dir) + cmd = "humann2_databases --download %s %s %s" % (database, + build, + db_target_dir) + subprocess.check_call(cmd, shell=True) + print(os.listdir(db_target_dir)) + os.rename(os.path.join(db_target_dir, database), build_target_dir) + print(os.listdir(db_target_dir)) + add_data_table_entry( + data_tables, + table_name, + dict( + dbkey=build, + value=value, + name=HUMANN2_REFERENCE_DATA[build], + path=build_target_dir)) + + +if __name__ == "__main__": + print("Starting...") + + # Read command line + parser = optparse.OptionParser(description='Download HUMAnN2 database') + parser.add_option('--database', help="Database name") + parser.add_option('--build', help="Build of the database") + options, args = parser.parse_args() + print("args : %s" % args) + + # Check for JSON file + if len(args) != 1: + sys.stderr.write("Need to supply JSON file name") + sys.exit(1) + + jsonfile = args[0] + + # Read the input JSON + params, target_dir = read_input_json(jsonfile) + + # Make the target directory + print("Making %s" % target_dir) + os.mkdir(target_dir) + + # Set up data tables dictionary + data_tables = create_data_tables_dict() + + if options.database == "chocophlan": + table_name = 'humann2_nucleotide_database' + else: + table_name = 'humann2_protein_database' + add_data_table(data_tables, table_name) + + # Fetch data from specified data sources + download_humann2_db( + data_tables, + table_name, + options.database, + options.build, + target_dir) + + # Write output JSON + print("Outputting JSON") + print(str(json.dumps(data_tables))) + open(jsonfile, 'wb').write(json.dumps(data_tables)) + print("Done.") |
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| diff -r 000000000000 -r 048593e41359 data_manager/data_manager_humann2_download.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_humann2_download.xml Sun Mar 12 14:33:34 2017 -0400 |
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| @@ -0,0 +1,56 @@ +<tool id="data_manager_humann2_download" name="HUMAnN2 download" version="0.9.9" tool_type="manage_data"> + <description>Download HUMAnN2 database</description> + <requirements> + <requirement type="package" version="0.9.9">humann2</requirement> + </requirements> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <command interpreter="python"> + data_manager_humann2_download.py + --database '$db.database' + --build '$db.build' + '${out_file}' + </command> + <inputs> + <conditional name="db"> + <param name="database" type="select" label="Type of database to download"> + <option value="chocophlan" selected="true">Nucleotide database</option> + <option value="uniref">Protein database</option> + </param> + <when value="chocophlan"> + <param name="build" type="select" label="Build for nucleotide database"> + <option value="full" selected="true">Full</option> + <option value="DEMO">Demo</option> + </param> + </when> + <when value="uniref"> + <param name="build" type="select" label="Build for protein database"> + <option value="uniref50_diamond">Full UniRef50</option> + <option value="uniref50_ec_filtered_diamond">EC-filtered UniRef50</option> + <option value="uniref50_GO_filtered_rapsearch2">GO filtered UniRef50 for rapsearch2</option> + <option value="uniref90_diamond" selected="true">Full UniRef50</option> + <option value="uniref90_ec_filtered_diamond">EC-filtered UniRef90</option> + <option value="DEMO_diamond">Demo</option> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" label="${tool.name}"/> + </outputs> + <tests> + </tests> + <help> + +This tool downloads the HUMAnN2 databases. + +`Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_. + + </help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1003153</citation> + <yield /> + </citations> +</tool> |
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| diff -r 000000000000 -r 048593e41359 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Sun Mar 12 14:33:34 2017 -0400 |
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| @@ -0,0 +1,34 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_humann2_download.xml" id="data_manager_humann2_download" > + <data_table name="humann2_nucleotide_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}">humann2/data/nucleotide_database/${dbkey}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/humann2/data/nucleotide_database/${dbkey}</value_translation> + </column> + </output> + </data_table> + <data_table name="humann2_protein_database"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="dbkey" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="path" output_ref="out_file" > + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">humann2/data/protein_database/${dbkey}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/humann2/data/protein_database/${dbkey}</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> + |
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| diff -r 000000000000 -r 048593e41359 tool-data/humann2_nucleotide_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/humann2_nucleotide_database.loc.sample Sun Mar 12 14:33:34 2017 -0400 |
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| @@ -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 ChocoPhlAn chocophlan /path/to/data \ No newline at end of file |
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| diff -r 000000000000 -r 048593e41359 tool-data/humann2_protein_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/humann2_protein_database.loc.sample Sun Mar 12 14:33:34 2017 -0400 |
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| @@ -0,0 +1,8 @@ +#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 Full UniRef50 uniref50_diamond /path/to/data +#02_16_2014 EC-filtered UniRef50 uniref50_ec_filtered_diamond /path/to/data +#02_16_2014 GO filtered UniRef50 for rapsearch2 uniref50_GO_filtered_rapsearch2 /path/to/data +#02_16_2014 Full UniRef90 uniref90_diamond /path/to/data +#02_16_2014 EC-filtered UniRef90 uniref90_ec_filtered_diamond /path/to/data \ No newline at end of file |
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| diff -r 000000000000 -r 048593e41359 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Mar 12 14:33:34 2017 -0400 |
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| @@ -0,0 +1,10 @@ +<tables> + <table name="humann2_nucleotide_database" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool-data/humann2_nucleotide_database.loc" /> + </table> + <table name="humann2_protein_database" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool-data/humann2_protein_database.loc" /> + </table> +</tables> |