# HG changeset patch
# User iuc
# Date 1637137376 0
# Node ID 5f9d6aee2256c4c312842d70c55f68fdb8d1ab9e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_malt_index_builder commit 710e56e0e522b0ed060dab2fecf05ed1c79c928f"
diff -r 000000000000 -r 5f9d6aee2256 data_manager/malt_index_builder.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/malt_index_builder.py Wed Nov 17 08:22:56 2021 +0000
@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+
+import json
+import optparse
+import os
+import subprocess
+import sys
+
+
+def get_id_name(params, dbkey, fasta_description=None):
+ sequence_id = params['param_dict']['sequence_id']
+ if not sequence_id:
+ sequence_id = dbkey
+
+ sequence_name = params['param_dict']['sequence_name']
+ if not sequence_name:
+ sequence_name = fasta_description
+ if not sequence_name:
+ sequence_name = dbkey
+ return sequence_id, sequence_name
+
+
+def build_malt_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, sequence_type, shapes, max_hits_per_seed, protein_reduct):
+ # The malt-build program produces a directory of files,
+ # so the data table path entry will be a directory and
+ # not an index file.
+ fasta_base_name = os.path.split(fasta_filename)[-1]
+ sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
+ os.symlink(fasta_filename, sym_linked_fasta_filename)
+ args = ['malt-build', '--input', sym_linked_fasta_filename, '--sequenceType', sequence_type, '--index', target_directory]
+ threads = os.environ.get('GALAXY_SLOTS')
+ if threads:
+ args.extend(['--threads', threads])
+ if shapes is not None:
+ args.extend(['--shapes', shapes])
+ if max_hits_per_seed is not None:
+ args.extend(['--maxHitsPerSeed', max_hits_per_seed])
+ if protein_reduct is not None:
+ args.extend(['--proteinReduct', protein_reduct])
+ proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
+ return_code = proc.wait()
+ if return_code:
+ sys.exit('Error building index, return_code: %d' % return_code)
+ # Remove unwanted files from the output directory.
+ os.remove(sym_linked_fasta_filename)
+ # The path entry here is the directory
+ # where the index files will be located,
+ # not a single index file (malt-build
+ # produces a directory if files, which
+ # is considered an index..
+ data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=None)
+ _add_data_table_entry(data_manager_dict, data_table_entry)
+
+
+def _add_data_table_entry(data_manager_dict, data_table_entry):
+ data_table_name = "malt_indices"
+ data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+ data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
+ data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
+ return data_manager_dict
+
+
+def main():
+ parser = optparse.OptionParser()
+ parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", help='fasta filename')
+ parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", help='fasta dbkey')
+ parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta description')
+ parser.add_option('-e', '--sequence_type', dest='sequence_type', action='store', type="string", help='DNA or Protein sequences')
+ parser.add_option('-p', '--shapes', dest='shapes', action='store', type="string", default=None, help='Comma-separated list of seed shapes')
+ parser.add_option('-m', '--max_hits_per_seed', dest='max_hits_per_seed', action='store', type="string", default=None, help='Maximum number of hits per seed')
+ parser.add_option('-r', '--protein_reduct', dest='protein_reduct', action='store', type="string", default=None, help='Name or definition of protein alphabet reduction')
+ (options, args) = parser.parse_args()
+
+ filename = args[0]
+
+ with open(filename) as fh:
+ params = json.load(fh)
+ target_directory = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_directory)
+ data_manager_dict = {}
+
+ dbkey = options.fasta_dbkey
+
+ if dbkey in [None, '', '?']:
+ raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
+
+ sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
+
+ # Build the index.
+ build_malt_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.sequence_type, options.shapes, options.max_hits_per_seed, options.protein_reduct)
+
+ # Save info to json file.
+ with open(filename, 'w') as fh:
+ json.dump(data_manager_dict, fh, sort_keys=True)
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 5f9d6aee2256 data_manager/malt_index_builder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/malt_index_builder.xml Wed Nov 17 08:22:56 2021 +0000
@@ -0,0 +1,131 @@
+
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+ python
+ malt
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+ 0.5.3
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+.. class:: infomark
+
+**Notice:** Values for Name and ID of sequence will be generated automatically if left blank.
+
+**What it does**
+
+Takes a reference sequence database (represented by a FastA file, possibly in gzip format) as input and produces an index that
+can be used by the malt tool as input. If MALT is to be used as a taxonomic and/or functional analysis tool as well as an
+alignment tool, then this MALT index builder tool must be provided with a number of mapping files that are used to map reference
+sequences to taxonomic or functional classes or to locate genes in DNA reference sequences.
+
+**Options**
+
+ * **Specify protein alphabet reduction** - specify the alphabet reduction in the case of protein reference sequences.
+ * **Specify seed settings** - specify the settings for controlling how MALT uses its seed-and-extend approach based on “spaced seeds”.
+
+ * **Shapes** - specify the seed shapes used. For DNA sequences, the default seed shape is: 111110111011110110111111. For protein sequences, by default MALT uses the following four shapes: 111101101110111, 1111000101011001111, 11101001001000100101111 and 11101001000010100010100111.
+ * **Maximim hits per seed** - specify the maximum number of hits per seed - MALT uses this to calculate a maximum number of hits per hash value.
+
+
+
+ https://doi.org/10.1101/050559
+
+
diff -r 000000000000 -r 5f9d6aee2256 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Wed Nov 17 08:22:56 2021 +0000
@@ -0,0 +1,18 @@
+
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diff -r 000000000000 -r 5f9d6aee2256 test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Wed Nov 17 08:22:56 2021 +0000
@@ -0,0 +1,19 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
+phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta
diff -r 000000000000 -r 5f9d6aee2256 test-data/malt_index_builder1.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/malt_index_builder1.json Wed Nov 17 08:22:56 2021 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"malt_indices": [{"dbkey": "phiX174", "name": "Pretty name for phiX174", "path": null, "value": "phiX174-1"}]}}
\ No newline at end of file
diff -r 000000000000 -r 5f9d6aee2256 test-data/malt_index_builder2.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/malt_index_builder2.json Wed Nov 17 08:22:56 2021 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"malt_indices": [{"dbkey": "phiX174", "name": "Pretty name for phiX174", "path": null, "value": "phiX174-2"}]}}
\ No newline at end of file
diff -r 000000000000 -r 5f9d6aee2256 test-data/malt_indices.loc
diff -r 000000000000 -r 5f9d6aee2256 test-data/phiX174.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174.fasta Wed Nov 17 08:22:56 2021 +0000
@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+
diff -r 000000000000 -r 5f9d6aee2256 tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Wed Nov 17 08:22:56 2021 +0000
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 000000000000 -r 5f9d6aee2256 tool-data/malt_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/malt_indices.loc.sample Wed Nov 17 08:22:56 2021 +0000
@@ -0,0 +1,23 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use a directory of MALT indexed data files. The malt_index.loc
+# file has this format (longer white space characters are TAB characters):
+#
+#
+#
+# So, for example, if you have the phiX indexe stored in
+# /depot/data2/galaxy/phiX/base/,
+# then the malt_index.loc entry would look like this:
+#
+# phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base
+#
+# and your /depot/data2/galaxy/phiX/base/ directory
+# would contain MALT index files for phiX174, sommething like this:
+#
+# -rw-r----- 1 galaxy galaxy 69 Oct 15 09:51 index0.idx
+# -rw-r----- 1 galaxy galaxy 5442 Oct 15 09:51 ref.db
+# -rw-r----- 1 galaxy galaxy 8 Oct 15 09:51 ref.idx
+# -rw-r----- 1 galaxy galaxy 25 Oct 15 09:51 ref.inf
+# -rw-r----- 1 galaxy galaxy 24952 Oct 15 09:51 table0.db
+# -rw-r----- 1 galaxy galaxy 65536 Oct 15 09:51 table0.idx
+#
+phiX174 NC_001422 Coliphage phiX174 /depot/data2/galaxy/tool-data/malt_index/phiX174
diff -r 000000000000 -r 5f9d6aee2256 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Nov 17 08:22:56 2021 +0000
@@ -0,0 +1,7 @@
+
+
+