| Next changeset 1:aec831b54a5b (2019-11-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea |
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added:
README data_manager/data_manager_fetch_mothur_reference_data.xml data_manager/fetch_mothur_reference_data.py data_manager_conf.xml tool-data/mothur_aligndb.loc.sample tool-data/mothur_lookup.loc.sample tool-data/mothur_map.loc.sample tool-data/mothur_taxonomy.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r ab7a7e798c34 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Nov 06 06:21:50 2017 -0500 |
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| @@ -0,0 +1,3 @@ +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 |
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| diff -r 000000000000 -r ab7a7e798c34 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 Mon Nov 06 06:21:50 2017 -0500 |
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| @@ -0,0 +1,132 @@ +<?xml version="1.0"?> +<tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.3" tool_type="manage_data"> + <description>Fetch and install reference data for Mothur</description> + <requirements> + <requirement type="package" version="2.7">python</requirement> + </requirements> + <command><![CDATA[ + python '$__tool_directory__/fetch_mothur_reference_data.py' + --source=$data_source.data_source_selector + #if str( $data_source.data_source_selector ) == "mothur_website" + --datasets '${data_source.ref_data}' + #elif str( $data_source.data_source_selector ) == "filesystem_paths" + --description '${data_source.description}' + --paths '${data_source.paths}' + #if $data_source.create_symlink + --link + #end if + #end if + '${out_file}' + ]]></command> + <inputs> + <conditional name="data_source"> + <param name="data_source_selector" type="select" + label="Choose the source for the reference data"> + <option value="mothur_website">Mothur website</option> + <option value="filesystem_paths">Filesystem paths</option> + </param> + <when value="mothur_website"> + <param name="ref_data" type="select" display="checkboxes" multiple="true" + label="Reference dataset to install"> + <option value="lookup_titanium">GS FLX Titanium lookup files</option> + <option value="lookup_gsflx">GSFLX lookup files</option> + <option value="lookup_gs20">GS20 lookup files</option> + <option value="RDP_v16">RDP reference files (training set version 16)</option> + <option value="RDP_v14">RDP reference files (training set version 14)</option> + <option value="RDP_v10">RDP reference files (training set version 10)</option> + <option value="RDP_v9">RDP reference files (training set version 9)</option> + <option value="RDP_v7">RDP reference files (training set version 7)</option> + <option value="RDP_v6">RDP reference files (training set version 6)</option> + <option value="silva_release_128">SILVA reference files (release 128)</option> + <option value="silva_release_123">SILVA reference files (release 123)</option> + <option value="silva_release_119">SILVA reference files (release 119)</option> + <option value="silva_release_102">SILVA reference files (release 102)</option> + <option value="greengenes_August2013">Greengenes reference taxonomy and alignment v13.8 (August 2013)</option> + <option value="greengenes_May2013">Greengenes reference taxonomy and alignment v13.5 (May 2013)</option> + <option value="greengenes_old">Greengenes reference taxonomy and alignment (pre-May 2013)</option> + <option value="greengenes_gold_alignment">Greengenes gold alignment</option> + <option value="secondary_structure_maps_silva">SILVA secondary structure maps</option> + <option value="secondary_structure_maps_greengenes">Greengenes secondary structure maps</option> + </param> + </when> + <when value="filesystem_paths"> + <param name="description" type="text" value="" size="50" + label="Description of the data" optional="False" /> + <param name="paths" type="text" value="" area="True" size="10x50" + label="Paths to upload" optional="False" + help="Upload all files pasted in the box. The (recursive) contents of any pasted directories will be added as well." /> + <param type="boolean" name="create_symlink" truevalue="create_symlink" + falsevalue="copy_file" + label="Create symlinks to data instead of copying into Galaxy" checked="on" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <tests> + <test> + <param name="data_sourece|ref_data" value="lookup_titanium"/> + <output name="out_file"> + <assert_contents> + <has_text text="GS FLX Titanium" /> + <has_text text="LookUp_Titanium.pat" /> + </assert_contents> + </output> + </test> + </tests> + <help> +.. 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. + + </help> +</tool> |
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| diff -r 000000000000 -r ab7a7e798c34 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 Mon Nov 06 06:21:50 2017 -0500 |
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| b'@@ -0,0 +1,560 @@\n+#!/usr/bin/env python\n+#\n+# Data manager for reference data for the \'mothur_toolsuite\' Galaxy tools\n+import json\n+import optparse\n+import os\n+import shutil\n+import sys\n+import tarfile\n+import tempfile\n+import urllib2\n+import zipfile\n+\n+# When extracting files from archives, skip names that\n+# start with the following strings\n+IGNORE_PATHS = (\'.\', \'__MACOSX/\', \'__\')\n+\n+# Map file extensions to data table names\n+MOTHUR_FILE_TYPES = {".map": "map",\n+ ".fasta": "aligndb",\n+ ".align": "aligndb",\n+ ".pat": "lookup",\n+ ".tax": "taxonomy"}\n+\n+# Reference data URLs\n+MOTHUR_REFERENCE_DATA = {\n+ # Look up data\n+ # http://www.mothur.org/wiki/Lookup_files\n+ "lookup_titanium": {\n+ "GS FLX Titanium": ["http://www.mothur.org/w/images/9/96/LookUp_Titanium.zip", ]\n+ },\n+ "lookup_gsflx": {\n+ "GSFLX": ["http://www.mothur.org/w/images/8/84/LookUp_GSFLX.zip", ]\n+ },\n+ "lookup_gs20": {\n+ "GS20": ["http://www.mothur.org/w/images/7/7b/LookUp_GS20.zip", ]\n+ },\n+ # RDP reference files\n+ # http://www.mothur.org/wiki/RDP_reference_files\n+ "RDP_v16": {\n+ "16S rRNA RDP training set 16":\n+ ["https://mothur.org/w/images/d/dc/Trainset16_022016.rdp.tgz", ],\n+ "16S rRNA PDS training set 16":\n+ ["https://mothur.org/w/images/c/c3/Trainset16_022016.pds.tgz", ],\n+ },\n+ "RDP_v14": {\n+ "16S rRNA RDP training set 14":\n+ ["https://mothur.org/w/images/6/6c/Trainset14_032015.rdp.tgz", ],\n+ "16S rRNA PDS training set 14":\n+ ["https://mothur.org/w/images/8/88/Trainset14_032015.pds.tgz", ],\n+ },\n+ "RDP_v10": {\n+ "16S rRNA RDP training set 10":\n+ ["http://www.mothur.org/w/images/b/b5/Trainset10_082014.rdp.tgz", ],\n+ "16S rRNA PDS training set 10":\n+ ["http://www.mothur.org/w/images/2/24/Trainset10_082014.pds.tgz", ],\n+ },\n+ "RDP_v9": {\n+ "16S rRNA RDP training set 9":\n+ ["http://www.mothur.org/w/images/7/72/Trainset9_032012.rdp.zip", ],\n+ "16S rRNA PDS training set 9":\n+ ["http://www.mothur.org/w/images/5/59/Trainset9_032012.pds.zip", ],\n+ },\n+ "RDP_v7": {\n+ "16S rRNA RDP training set 7":\n+ ["http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip", ],\n+ "16S rRNA PDS training set 7":\n+ ["http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip", ],\n+ "8S rRNA Fungi training set 7":\n+ ["http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip", ],\n+ },\n+ "RDP_v6": {\n+ "RDP training set 6":\n+ ["http://www.mothur.org/w/images/4/49/RDPTrainingSet.zip", ],\n+ },\n+ # Silva reference files\n+ # http://www.mothur.org/wiki/Silva_reference_files\n+ "silva_release_128": {\n+ "SILVA release 128":\n+ ["https://mothur.org/w/images/b/b4/Silva.nr_v128.tgz",\n+ "https://mothur.org/w/images/a/a4/Silva.seed_v128.tgz", ],\n+ },\n+ "silva_release_123": {\n+ "SILVA release 123":\n+ ["https://mothur.org/w/images/b/be/Silva.nr_v123.tgz",\n+ "https://mothur.org/w/images/1/15/Silva.seed_v123.tgz", ],\n+ },\n+ "silva_release_119": {\n+ "SILVA release 119":\n+ ["http://www.mothur.org/w/images/2/27/Silva.nr_v119.tgz",\n+ "http://www.mothur.org/w/images/5/56/Silva.seed_v119.tgz", ],\n+ },\n+ "silva_release_102": {\n+ "SILVA release 102":\n+ ["http://www.mothur.org/w/images/9/98/Silva.bacteria.zip",\n+ "http://www.mothur.org/w/images/3/3c/Silva.archaea.zip",\n+ "http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip", ],\n+ },\n+ "silva_gold_bacteria": {\n+ "SILVA gold":\n+ ["http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip", ],\n+ },\n+ # Greengenes\n+ # http://www.mothur.org/wiki/Greengenes-formatted_databases\n+ "greengenes_August2013": {\n+ "Greengenes August 2013":\n+ ["http://www.mothur.org/w/imag'..b'th.join(path, f), )))\n+ else:\n+ print "Not a file or directory, ignored"\n+ return files\n+\n+\n+def import_from_server(data_tables, target_dir, paths, description, link_to_data=False):\n+ """Import reference data from filesystem paths\n+\n+ Creates references to the specified file(s) on the Galaxy\n+ server in the appropriate data table (determined from the\n+ file extension).\n+\n+ The \'data_tables\' dictionary should have been created using\n+ the \'create_data_tables_dict\' and \'add_data_table\' functions.\n+\n+ Arguments:\n+ data_tables: a dictionary containing the data table info\n+ target_dir: directory to put copy or link to the data file\n+ paths: list of file and/or directory paths to import\n+ description: text to associate with the files\n+ link_to_data: boolean, if False then copy the data file\n+ into Galaxy (default); if True then make a symlink to\n+ the data file\n+\n+ """\n+ # Collect list of files based on input paths\n+ files = files_from_filesystem_paths(paths)\n+ # Handle each file individually\n+ for f in files:\n+ type_ = identify_type(f)\n+ if type_ is None:\n+ print "%s: unrecognised type, skipped" % f\n+ continue\n+ ref_data_file = os.path.basename(f)\n+ target_file = os.path.join(target_dir, ref_data_file)\n+ entry_name = "%s" % os.path.splitext(ref_data_file)[0]\n+ if description:\n+ entry_name += " (%s)" % description\n+ print "%s\\t\\\'%s\'\\t.../%s" % (type_, entry_name, ref_data_file)\n+ # Link to or copy the data\n+ if link_to_data:\n+ os.symlink(f, target_file)\n+ else:\n+ shutil.copyfile(f, target_file)\n+ # Add entry to data table\n+ table_name = "mothur_%s" % type_\n+ add_data_table_entry(data_tables, table_name, dict(name=entry_name, value=ref_data_file))\n+\n+\n+if __name__ == "__main__":\n+ print "Starting..."\n+\n+ # Read command line\n+ parser = optparse.OptionParser()\n+ parser.add_option(\'--source\', action=\'store\', dest=\'data_source\')\n+ parser.add_option(\'--datasets\', action=\'store\', dest=\'datasets\', default=\'\')\n+ parser.add_option(\'--paths\', action=\'store\', dest=\'paths\', default=[])\n+ parser.add_option(\'--description\', action=\'store\', dest=\'description\', default=\'\')\n+ parser.add_option(\'--link\', action=\'store_true\', dest=\'link_to_data\')\n+ options, args = parser.parse_args()\n+ print "options: %s" % options\n+ print "args : %s" % args\n+\n+ # Check for JSON file\n+ if len(args) != 1:\n+ sys.stderr.write("Need to supply JSON file name")\n+ sys.exit(1)\n+\n+ jsonfile = args[0]\n+\n+ # Read the input JSON\n+ params, target_dir = read_input_json(jsonfile)\n+\n+ # Make the target directory\n+ print "Making %s" % target_dir\n+ os.mkdir(target_dir)\n+\n+ # Set up data tables dictionary\n+ data_tables = create_data_tables_dict()\n+ add_data_table(data_tables, \'mothur_lookup\')\n+ add_data_table(data_tables, \'mothur_aligndb\')\n+ add_data_table(data_tables, \'mothur_map\')\n+ add_data_table(data_tables, \'mothur_taxonomy\')\n+\n+ # Fetch data from specified data sources\n+ if options.data_source == \'mothur_website\':\n+ datasets = options.datasets.split(\',\')\n+ fetch_from_mothur_website(data_tables, target_dir, datasets)\n+ elif options.data_source == \'filesystem_paths\':\n+ # Check description text\n+ description = options.description.strip()\n+ # Get list of paths (need to remove any escapes for \'\\n\' and \'\\r\'\n+ # that might have been inserted by Galaxy)\n+ paths = options.paths.replace(\'__cn__\', \'\\n\').replace(\'__cr__\', \'\\r\').split()\n+ import_from_server(data_tables, target_dir, paths, description, link_to_data=options.link_to_data)\n+ # Write output JSON\n+ print "Outputting JSON"\n+ print str(json.dumps(data_tables))\n+ open(jsonfile, \'wb\').write(json.dumps(data_tables))\n+ print "Done."\n' |
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| diff -r 000000000000 -r ab7a7e798c34 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Mon Nov 06 06:21:50 2017 -0500 |
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| @@ -0,0 +1,57 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_fetch_mothur_reference_data.xml" id="data_manager_mothur_fetch_reference_data"> + <data_table name="mothur_aligndb"> + <output> + <column name="name" /> + <column name="value" output_ref="out_file" > + <move type="file"> + <source>${value}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mothur/aligndb/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mothur/aligndb/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="mothur_lookup"> + <output> + <column name="name" /> + <column name="value" output_ref="out_file" > + <move type="file"> + <source>${value}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mothur/lookup/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mothur/lookup/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="mothur_map"> + <output> + <column name="name" /> + <column name="value" output_ref="out_file" > + <move type="file"> + <source>${value}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mothur/map/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mothur/map/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="mothur_taxonomy"> + <output> + <column name="name" /> + <column name="value" output_ref="out_file" > + <move type="file"> + <source>${value}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mothur/taxonomy/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mothur/taxonomy/${value}</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 ab7a7e798c34 tool-data/mothur_aligndb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mothur_aligndb.loc.sample Mon Nov 06 06:21:50 2017 -0500 |
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| @@ -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 +# +#<dbname> <file_base> +# +#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 |
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| diff -r 000000000000 -r ab7a7e798c34 tool-data/mothur_lookup.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mothur_lookup.loc.sample Mon Nov 06 06:21:50 2017 -0500 |
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| @@ -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 +# +#<name> <file_base> +# +#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 |
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| diff -r 000000000000 -r ab7a7e798c34 tool-data/mothur_map.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mothur_map.loc.sample Mon Nov 06 06:21:50 2017 -0500 |
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| @@ -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 +# +#<name> <file_base> +# +#greengenes /project/db/galaxy/mothur/gg.ss.map +#silva /project/db/galaxy/mothur/silva.ss.map |
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| diff -r 000000000000 -r ab7a7e798c34 tool-data/mothur_taxonomy.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mothur_taxonomy.loc.sample Mon Nov 06 06:21:50 2017 -0500 |
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| @@ -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 +# +#<taxonomyname> <file_base> +# +#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 +# |
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| diff -r 000000000000 -r ab7a7e798c34 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Nov 06 06:21:50 2017 -0500 |
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| @@ -0,0 +1,18 @@ +<tables> + <table name="mothur_aligndb" comment_char="#" allow_duplicate_entries="False"> + <columns>name, value</columns> + <file path="tool-data/mothur_aligndb.loc" /> + </table> + <table name="mothur_lookup" comment_char="#" allow_duplicate_entries="False"> + <columns>name, value</columns> + <file path="tool-data/mothur_lookup.loc" /> + </table> + <table name="mothur_map" comment_char="#" allow_duplicate_entries="False"> + <columns>name, value</columns> + <file path="tool-data/mothur_map.loc" /> + </table> + <table name="mothur_taxonomy" comment_char="#" allow_duplicate_entries="False"> + <columns>name, value</columns> + <file path="tool-data/mothur_taxonomy.loc" /> + </table> +</tables> |