--- /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>