# HG changeset patch
# User rhpvorderman
# Date 1624363661 0
# Node ID 3f6f7ca5f95a67216c282ca530c17ecfc37750e3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit 821349cd1c414dcad2128ba78d2b9d9051b3e75b"
diff -r 000000000000 -r 3f6f7ca5f95a README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Tue Jun 22 12:07:41 2021 +0000
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+Data manager to install reference data for Mothur toolsuite
+
+Imported from https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/data_manager_mothur_toolsuite
diff -r 000000000000 -r 3f6f7ca5f95a data_manager/data_manager_fetch_mothur_reference_data.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_mothur_reference_data.xml Tue Jun 22 12:07:41 2021 +0000
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+ Fetch and install reference data for Mothur
+
+ python
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+.. class:: infomark
+
+**What it does**
+
+This tool fetches reference data used by the mothur_toolsuite set of Galaxy tools,
+and populates the appropriate data tables.
+
+The reference data can be imported directly from the Mothur website, or from files
+in a server directory.
+
+Files are added to the following data tables based on file extension:
+
+ * **mothur_lookup**: for .pat files
+ * **mothur_aligndb**: for .fasta files
+ * **mothur_map**: for .map files
+ * **mothur_taxonomy**: for .tax files
+
+------
+
+**Importing from Mothur website**
+
+Reference data sets provided by the Mothur developers can be downloaded from the
+Mothur website. See the following pages to get more information about each dataset:
+
+ * Lookup data: http://www.mothur.org/wiki/Lookup_files
+ * RDP reference data: http://www.mothur.org/wiki/RDP_reference_files
+ * Silva data: http://www.mothur.org/wiki/Silva_reference_files
+ * Greengenes data: http://www.mothur.org/wiki/Greengenes-formatted_databases
+ * Secondary structure maps: http://www.mothur.org/wiki/Secondary_structure_map
+
+**Importing from file system paths**
+
+If reference data is already on the server filesystem then use this option to
+import it into the Mothur data tables. The appropriate data tables are determined
+based on the file extensions.
+
+Optionally a description can be added which will appear next to the base of the
+reference file name in the data table entry.
+
+------
+
+.. class:: warningmark
+
+**A note on Lane masks**
+
+Lane mask data is also available via the Mothur website (files ending in ".filter"):
+
+ * http://www.mothur.org/wiki/Lane_mask
+
+but as these data are not currently used in the toolsuite, they cannot be imported
+using this data manager.
+
+
+
diff -r 000000000000 -r 3f6f7ca5f95a data_manager/fetch_mothur_reference_data.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/fetch_mothur_reference_data.py Tue Jun 22 12:07:41 2021 +0000
@@ -0,0 +1,580 @@
+#!/usr/bin/env python3
+#
+# Data manager for reference data for the 'mothur_toolsuite' Galaxy tools
+import json
+import optparse
+import os
+import shutil
+import sys
+import tarfile
+import tempfile
+import urllib.error
+import urllib.parse
+import urllib.request
+import zipfile
+from functools import reduce
+
+# When extracting files from archives, skip names that
+# start with the following strings
+IGNORE_PATHS = ('.', '__MACOSX/', '__')
+
+# Map file extensions to data table names
+MOTHUR_FILE_TYPES = {".map": "map",
+ ".fasta": "aligndb",
+ ".align": "aligndb",
+ ".pat": "lookup",
+ ".tax": "taxonomy"}
+
+# Reference data URLs
+MOTHUR_REFERENCE_DATA = {
+ # Look up data
+ # http://www.mothur.org/wiki/Lookup_files
+ "lookup_titanium": {
+ "GS FLX Titanium": ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lookup_titanium.zip", ]
+ },
+ "lookup_gsflx": {
+ "GSFLX": ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lookup_gsflx.zip", ]
+ },
+ "lookup_gs20": {
+ "GS20": ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lookup_gs20.zip", ]
+ },
+ # RDP reference files
+ # http://www.mothur.org/wiki/RDP_reference_files
+ "RDP_v18": {
+ "16S rRNA RDP training set 18":
+ [
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset18_062020.rdp.tgz", ],
+ "16S rRNA PDS training set 18":
+ [
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset18_062020.pds.tgz", ],
+ },
+ "RDP_v16": {
+ "16S rRNA RDP training set 16":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset16_022016.rdp.tgz", ],
+ "16S rRNA PDS training set 16":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset16_022016.pds.tgz", ],
+ },
+ "RDP_v14": {
+ "16S rRNA RDP training set 14":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset14_032015.rdp.tgz", ],
+ "16S rRNA PDS training set 14":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset14_032015.pds.tgz", ],
+ },
+ "RDP_v10": {
+ "16S rRNA RDP training set 10":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset10_082014.rdp.tgz", ],
+ "16S rRNA PDS training set 10":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset10_082014.pds.tgz", ],
+ },
+ "RDP_v9": {
+ "16S rRNA RDP training set 9":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset9_032012.rdp.zip", ],
+ "16S rRNA PDS training set 9":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset9_032012.pds.zip", ],
+ },
+ "RDP_v7": {
+ "16S rRNA RDP training set 7":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset7_112011.rdp.zip", ],
+ "16S rRNA PDS training set 7":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset7_112011.pds.zip", ],
+ "8S rRNA Fungi training set 7":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/fungilsu_train_v7.zip", ],
+ },
+ "RDP_v6": {
+ "RDP training set 6":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/rdptrainingset.zip", ],
+ },
+ # Silva reference files
+ # http://www.mothur.org/wiki/Silva_reference_files
+ "silva_release_138.1": {
+ "SILVA release 138.1":
+ [
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v138_1.tgz",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v138_1.tgz", ],
+ },
+ "silva_release_128": {
+ "SILVA release 128":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v128.tgz",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v128.tgz", ],
+ },
+ "silva_release_123": {
+ "SILVA release 123":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v123.tgz",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v123.tgz", ],
+ },
+ "silva_release_119": {
+ "SILVA release 119":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v119.tgz",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v119.tgz", ],
+ },
+ "silva_release_102": {
+ "SILVA release 102":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.bacteria.zip",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.archaea.zip",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.eukarya.zip", ],
+ },
+ "silva_gold_bacteria": {
+ "SILVA gold":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.gold.bacteria.zip", ],
+ },
+ # Greengenes
+ # http://www.mothur.org/wiki/Greengenes-formatted_databases
+ "greengenes_August2013": {
+ "Greengenes August 2013":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_8_99.refalign.tgz",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_8_99.taxonomy.tgz", ],
+ },
+ "greengenes_May2013": {
+ "Greengenes May 2013":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_5_99.refalign.tgz",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_5_99.taxonomy.tgz", ],
+ },
+ "greengenes_old": {
+ "Greengenes pre-May 2013":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/greengenes.alignment.zip",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/greengenes.tax.tgz", ],
+ },
+ "greengenes_gold_alignment": {
+ "Greengenes gold alignment":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/greengenes.gold.alignment.zip", ],
+ },
+ # Secondary structure maps
+ # http://www.mothur.org/wiki/Secondary_structure_map
+ "secondary_structure_maps_silva": {
+ "SILVA":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva_ss_map.zip", ],
+ },
+ "secondary_structure_maps_greengenes": {
+ "Greengenes":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_ss_map.zip", ],
+ },
+ # Lane masks: not used here?
+ "lane_masks": {
+ "Greengenes-compatible":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/Lane1241.gg.filter",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/lane1287.gg.filter",
+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/lane1349.gg.filter", ],
+ "SILVA-compatible":
+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lane1349.silva.filter", ]
+ },
+}
+
+
+# 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.
+
+ """
+ with open(jsonfile) as fh:
+ params = json.load(fh)
+ 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(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)
+
+
+# Utility functions for downloading and unpacking archive files
+def download_file(url, target=None, wd=None):
+ """Download a file from a URL
+
+ Fetches a file from the specified URL.
+
+ If 'target' is specified then the file is saved to this
+ name; otherwise it's saved as the basename of the URL.
+
+ If 'wd' is specified then it is used as the 'working
+ directory' where the file will be save on the local
+ system.
+
+ Returns the name that the file is saved with.
+
+ """
+ print(("Downloading %s" % url))
+ if not target:
+ target = os.path.basename(url)
+ if wd:
+ target = os.path.join(wd, target)
+ print(("Saving to %s" % target))
+ with open(target, 'wb') as fh:
+ fh.write(urllib.request.urlopen(url).read())
+ return target
+
+
+def unpack_zip_archive(filen, wd=None):
+ """Extract files from a ZIP archive
+
+ Given a ZIP archive, extract the files it contains
+ and return a list of the resulting file names and
+ paths.
+
+ 'wd' specifies the working directory to extract
+ the files to, otherwise they are extracted to the
+ current working directory.
+
+ Once all the files are extracted the ZIP archive
+ file is deleted from the file system.
+
+ """
+ if not zipfile.is_zipfile(filen):
+ print("%s: not ZIP formatted file")
+ return [filen]
+ file_list = []
+ with zipfile.ZipFile(filen) as z:
+ for name in z.namelist():
+ if reduce(lambda x, y: x or name.startswith(y), IGNORE_PATHS, False):
+ print(("Ignoring %s" % name))
+ continue
+ if wd:
+ target = os.path.join(wd, name)
+ else:
+ target = name
+ if name.endswith('/'):
+ # Make directory
+ print(("Creating dir %s" % target))
+ try:
+ os.makedirs(target)
+ except OSError:
+ pass
+ else:
+ # Extract file
+ print(("Extracting %s" % name))
+ try:
+ os.makedirs(os.path.dirname(target))
+ except OSError:
+ pass
+ with open(target, 'wb') as fh:
+ fh.write(z.read(name))
+ file_list.append(target)
+ print(("Removing %s" % filen))
+ os.remove(filen)
+ return file_list
+
+
+def unpack_tar_archive(filen, wd=None):
+ """Extract files from a TAR archive
+
+ Given a TAR archive (which optionally can be
+ compressed with either gzip or bz2), extract the
+ files it contains and return a list of the
+ resulting file names and paths.
+
+ 'wd' specifies the working directory to extract
+ the files to, otherwise they are extracted to the
+ current working directory.
+
+ Once all the files are extracted the TAR archive
+ file is deleted from the file system.
+
+ """
+ file_list = []
+ if not tarfile.is_tarfile(filen):
+ print("%s: not TAR file")
+ return [filen]
+ with tarfile.open(filen) as t:
+ for name in t.getnames():
+ # Check for unwanted files
+ if reduce(lambda x, y: x or name.startswith(y), IGNORE_PATHS, False):
+ print(("Ignoring %s" % name))
+ continue
+ # Extract file
+ print(("Extracting %s" % name))
+ t.extract(name, wd)
+ if wd:
+ target = os.path.join(wd, name)
+ else:
+ target = name
+ file_list.append(target)
+ print(("Removing %s" % filen))
+ os.remove(filen)
+ return file_list
+
+
+def unpack_archive(filen, wd=None):
+ """Extract files from an archive
+
+ Wrapper function that calls the appropriate
+ unpacking function depending on the archive
+ type, and returns a list of files that have
+ been extracted.
+
+ 'wd' specifies the working directory to extract
+ the files to, otherwise they are extracted to the
+ current working directory.
+
+ """
+ print(("Unpack %s" % filen))
+ ext = os.path.splitext(filen)[1]
+ print(("Extension: %s" % ext))
+ if ext == ".zip":
+ return unpack_zip_archive(filen, wd=wd)
+ elif ext == ".tgz":
+ return unpack_tar_archive(filen, wd=wd)
+ else:
+ return [filen]
+
+
+def fetch_files(urls, wd=None, files=None):
+ """Download and unpack files from a list of URLs
+
+ Given a list of URLs, download and unpack each
+ one, and return a list of the extracted files.
+
+ 'wd' specifies the working directory to extract
+ the files to, otherwise they are extracted to the
+ current working directory.
+
+ If 'files' is given then the list of extracted
+ files will be appended to this list before being
+ returned.
+
+ """
+ if files is None:
+ files = []
+ for url in urls:
+ filen = download_file(url, wd=wd)
+ files.extend(unpack_archive(filen, wd=wd))
+ return files
+
+
+# Utility functions specific to the Mothur reference data
+def identify_type(filen):
+ """Return the data table name based on the file name
+
+ """
+ ext = os.path.splitext(filen)[1]
+ try:
+ return MOTHUR_FILE_TYPES[ext]
+ except KeyError:
+ print(("WARNING: unknown file type for " + filen + ", skipping"))
+ return None
+
+
+def get_name(filen):
+ """Generate a descriptive name based on the file name
+ """
+ # type_ = identify_type(filen)
+ name = os.path.splitext(os.path.basename(filen))[0]
+ for delim in ('.', '_'):
+ name = name.replace(delim, ' ')
+ return name
+
+
+def fetch_from_mothur_website(data_tables, target_dir, datasets):
+ """Fetch reference data from the Mothur website
+
+ For each dataset in the list 'datasets', download (and if
+ necessary unpack) the related files from the Mothur website,
+ copy them to the data manager's target directory, and add
+ references to the files to the appropriate data table.
+
+ 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
+ target_dir: directory to put the downloaded files
+ datasets: a list of dataset names corresponding to keys in
+ the MOTHUR_REFERENCE_DATA dictionary
+ """
+ # Make working dir
+ wd = tempfile.mkdtemp(suffix=".mothur", dir=os.getcwd())
+ print(("Working dir %s" % wd))
+ # Iterate over all requested reference data URLs
+ for dataset in datasets:
+ print(("Handling dataset '%s'" % dataset))
+ for name in MOTHUR_REFERENCE_DATA[dataset]:
+ for f in fetch_files(MOTHUR_REFERENCE_DATA[dataset][name], wd=wd):
+ type_ = identify_type(f)
+ entry_name = "%s (%s)" % (os.path.splitext(os.path.basename(f))[0], name)
+ print(("%s\t\'%s'\t.../%s" % (type_, entry_name, os.path.basename(f))))
+ if type_ is not None:
+ # Move to target dir
+ ref_data_file = os.path.basename(f)
+ f1 = os.path.join(target_dir, ref_data_file)
+ print(("Moving %s to %s" % (f, f1)))
+ shutil.move(f, f1)
+ # Add entry to data table
+ table_name = "mothur_%s" % type_
+ add_data_table_entry(data_tables, table_name, dict(name=entry_name, value=ref_data_file))
+ # Remove working dir
+ print(("Removing %s" % wd))
+ shutil.rmtree(wd)
+
+
+def files_from_filesystem_paths(paths):
+ """Return list of file paths from arbitrary input paths
+
+ Given a list of filesystem paths, return a list of
+ full paths corresponding to all files found recursively
+ from under those paths.
+
+ """
+ # Collect files to add
+ files = []
+ for path in paths:
+ path = os.path.abspath(path)
+ print(("Examining '%s'..." % path))
+ if os.path.isfile(path):
+ # Store full path for file
+ files.append(path)
+ elif os.path.isdir(path):
+ # Descend into directory and collect the files
+ for f in os.listdir(path):
+ files.extend(files_from_filesystem_paths((os.path.join(path, f), )))
+ else:
+ print("Not a file or directory, ignored")
+ return files
+
+
+def import_from_server(data_tables, target_dir, paths, description, link_to_data=False):
+ """Import reference data from filesystem paths
+
+ 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
+ target_dir: directory to put copy or link to the data file
+ paths: list of file and/or directory paths to import
+ description: text to associate with the files
+ link_to_data: boolean, if False then copy the data file
+ into Galaxy (default); if True then make a symlink to
+ the data file
+
+ """
+ # Collect list of files based on input paths
+ files = files_from_filesystem_paths(paths)
+ # Handle each file individually
+ for f in files:
+ type_ = identify_type(f)
+ if type_ is None:
+ print(("%s: unrecognised type, skipped" % f))
+ continue
+ ref_data_file = os.path.basename(f)
+ target_file = os.path.join(target_dir, ref_data_file)
+ entry_name = "%s" % os.path.splitext(ref_data_file)[0]
+ if description:
+ entry_name += " (%s)" % description
+ print(("%s\t\'%s'\t.../%s" % (type_, entry_name, ref_data_file)))
+ # Link to or copy the data
+ if link_to_data:
+ os.symlink(f, target_file)
+ else:
+ shutil.copyfile(f, target_file)
+ # Add entry to data table
+ table_name = "mothur_%s" % type_
+ add_data_table_entry(data_tables, table_name, dict(name=entry_name, value=ref_data_file))
+
+
+if __name__ == "__main__":
+ print("Starting...")
+
+ # Read command line
+ parser = optparse.OptionParser()
+ parser.add_option('--source', action='store', dest='data_source')
+ parser.add_option('--datasets', action='store', dest='datasets', default='')
+ parser.add_option('--paths', action='store', dest='paths', default=[])
+ parser.add_option('--description', action='store', dest='description', default='')
+ parser.add_option('--link', action='store_true', dest='link_to_data')
+ options, args = parser.parse_args()
+ print(("options: %s" % options))
+ 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()
+ add_data_table(data_tables, 'mothur_lookup')
+ add_data_table(data_tables, 'mothur_aligndb')
+ add_data_table(data_tables, 'mothur_map')
+ add_data_table(data_tables, 'mothur_taxonomy')
+
+ # Fetch data from specified data sources
+ if options.data_source == 'mothur_website':
+ datasets = options.datasets.split(',')
+ fetch_from_mothur_website(data_tables, target_dir, datasets)
+ elif options.data_source == 'filesystem_paths':
+ # Check description text
+ description = options.description.strip()
+ # Get list of paths (need to remove any escapes for '\n' and '\r'
+ # that might have been inserted by Galaxy)
+ paths = options.paths.replace('__cn__', '\n').replace('__cr__', '\r').split()
+ import_from_server(data_tables, target_dir, paths, description, link_to_data=options.link_to_data)
+ # Write output JSON
+ print("Outputting JSON")
+ with open(jsonfile, 'w') as fh:
+ json.dump(data_tables, fh, sort_keys=True)
+ print("Done.")
diff -r 000000000000 -r 3f6f7ca5f95a data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Tue Jun 22 12:07:41 2021 +0000
@@ -0,0 +1,57 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 3f6f7ca5f95a tool-data/mothur_aligndb.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mothur_aligndb.loc.sample Tue Jun 22 12:07:41 2021 +0000
@@ -0,0 +1,19 @@
+#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):
+#
+# Reference Alignments: http://www.mothur.org/wiki/Alignment_database
+#
+#
+#
+#greengenes /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
+#silva archaea /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta
+#silva bacteria /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
+#silva eukarya /project/db/galaxy/mothur/silva.eukarya.fasta
+#silva archaea nogap /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta
+#silva bacteria nogap /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta
+#silva eukarya nogap /project/db/galaxy/mothur/nogap.eukarya.fasta
+#FungiLSU_train_1400bp_8506_mod.fasta /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta
+#trainset6_032010.rdp.fasta /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta
+#trainset7_112011.pds.fasta /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
+#trainset7_112011.rdp.fasta /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
diff -r 000000000000 -r 3f6f7ca5f95a tool-data/mothur_lookup.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mothur_lookup.loc.sample Tue Jun 22 12:07:41 2021 +0000
@@ -0,0 +1,11 @@
+#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):
+#
+# lookup files from: http://www.mothur.org/wiki/Lookup_files
+#
+#
+#
+#GS20 /project/db/galaxy/mothur/lookup/LookUp_GS20.pat
+#GSFLX /project/db/galaxy/mothur/lookup/LookUp_GSFLX.pat
+#Titanium /project/db/galaxy/mothur/lookup/LookUp_Titanium.pat
diff -r 000000000000 -r 3f6f7ca5f95a tool-data/mothur_map.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mothur_map.loc.sample Tue Jun 22 12:07:41 2021 +0000
@@ -0,0 +1,10 @@
+#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):
+#
+# Secondary structure maps: http://www.mothur.org/wiki/Secondary_structure_map
+#
+#
+#
+#greengenes /project/db/galaxy/mothur/gg.ss.map
+#silva /project/db/galaxy/mothur/silva.ss.map
diff -r 000000000000 -r 3f6f7ca5f95a tool-data/mothur_taxonomy.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mothur_taxonomy.loc.sample Tue Jun 22 12:07:41 2021 +0000
@@ -0,0 +1,24 @@
+#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):
+#
+# Silva reference files: http://www.mothur.org/wiki/Silva_reference_files
+#
+#
+#
+#archaea.gg /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax
+#archaea.silva /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax
+#archaea.rdp /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax
+#archaea.ncbi /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax
+#bacteria.gg /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax
+#bacteria.silva /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax
+#bacteria.ncbi /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax
+#bacteria.rdp /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax
+#bacteria.rdp6 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax
+#eukarya.silva /project/db/galaxy/mothur/silva.eukarya.silva.tax
+#eukarya.ncbi /project/db/galaxy/mothur/silva.eukarya.ncbi.tax
+#trainset6_032010.rdp.tax /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax
+#trainset7_112011.pds.tax /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax
+#trainset7_112011.rdp.tax /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
+#FungiLSU_train_1400bp_8506_mod.tax /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax
+#
diff -r 000000000000 -r 3f6f7ca5f95a tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Jun 22 12:07:41 2021 +0000
@@ -0,0 +1,18 @@
+
+