Mercurial > repos > iuc > data_manager_malt_index_builder
changeset 0:5f9d6aee2256 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_malt_index_builder commit 710e56e0e522b0ed060dab2fecf05ed1c79c928f"
| author | iuc |
|---|---|
| date | Wed, 17 Nov 2021 08:22:56 +0000 |
| parents | |
| children | |
| files | data_manager/malt_index_builder.py data_manager/malt_index_builder.xml data_manager_conf.xml test-data/all_fasta.loc test-data/malt_index_builder1.json test-data/malt_index_builder2.json test-data/malt_indices.loc test-data/phiX174.fasta tool-data/all_fasta.loc.sample tool-data/malt_indices.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 11 files changed, 407 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /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()
--- /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 @@ +<tool id="data_manager_malt_index_builder" name="MALT index builder" tool_type="manage_data" version="@TOOL_VERSION@+galaxy0" profile="21.01"> + <description></description> + <requirements> + <requirement type="package" version="3.8">python</requirement> + <requirement type="package" version="0.53">malt</requirement> + </requirements> + <macros> + <token name="@TOOL_VERSION@">0.5.3</token> + </macros> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/malt_index_builder.py' +'${out_file}' +--fasta_filename '${all_fasta_source.fields.path}' +--fasta_dbkey '${all_fasta_source.fields.dbkey}' +--fasta_description '${all_fasta_source.fields.name}' +--sequence_type '${sequence_type}' +#if str($protein_reduct_setting_cond.protein_reduct_setting) == 'yes': + --protein_reduct '${protein_reduct_setting_cond.protein_reduct}' +#end if +#if str($seed_setting_cond.seed_setting) == 'yes': + --shapes '${seed_setting_cond.shapes}' + ## malt-build requires a string here. + --max_hits_per_seed '${seed_setting_cond.max_hits_per_seed}' +#end if + ]]></command> + <inputs> + <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + <param name="sequence_name" type="text" value="" label="Name of sequence"/> + <param name="sequence_id" type="text" value="" label="ID for sequence"/> + <param name="sequence_type" type="select" label="Reference sequences type" help="Use the DNA setting For RNA sequences"> + <option value="DNA" selected="true">DNA</option> + <option value="Protein">Protein</option> + </param> + <conditional name="protein_reduct_setting_cond"> + <param name="protein_reduct_setting" type="select" label="Specify protein alphabet reduction?" help="Used only if the reference sequences are Protein sequences"> + <option selected="true" value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="protein_reduct" type="select" label="Name or definition of protein alphabet reduction"> + <option selected="true" value="DIAMOND_11">DIAMOND_11</option> + <option value="BLOSUM50_10">BLOSUM50_10</option> + <option value="BLOSUM50_11">BLOSUM50_11</option> + <option value="BLOSUM50_15">BLOSUM50_15</option> + <option value="BLOSUM50_4">BLOSUM50_4</option> + <option value="BLOSUM50_8">BLOSUM50_8</option> + <option value="GBMR4">GBMR4</option> + <option value="HSDM17">HSDM17</option> + <option value="MALT_10">MALT_10</option> + <option value="SDM12">SDM12</option> + <option value="UNREDUCED">UNREDUCED</option> + </param> + </when> + </conditional> + <conditional name="seed_setting_cond"> + <param name="seed_setting" type="select" label="Specify seed settings?"> + <option selected="true" value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="shapes" type="text" value="" label="Comma-separated list of seed shapes" help="See help text below"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="'"'"'"/> + </mapping> + </sanitizer> + </param> + <param name="max_hits_per_seed" type="integer" value="1" min="1" label="Maximum number of hits per seed"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <tests> + <test> + <param name="all_fasta_source" value="phiX174"/> + <param name="sequence_name" value="Pretty name for phiX174"/> + <param name="sequence_id" value="phiX174-1"/> + <output name="out_file" value="malt_index_builder1.json"/> + </test> + <test> + <param name="all_fasta_source" value="phiX174"/> + <param name="sequence_name" value="Pretty name for phiX174"/> + <param name="sequence_id" value="phiX174-1"/> + <param name="seed_setting" value="yes"/> + <param name="shapes" value="111110111011110110111111"/> + <output name="out_file" value="malt_index_builder1.json"/> + </test> + <test> + <param name="all_fasta_source" value="phiX174"/> + <param name="sequence_name" value="Pretty name for phiX174"/> + <param name="sequence_id" value="phiX174-2"/> + <param name="sequence_type" value="Protein"/> + <param name="protein_reduct_setting" value="yes"/> + <param name="protein_reduct" value="BLOSUM50_10"/> + <output name="out_file" value="malt_index_builder2.json"/> + </test> + </tests> + <help> +.. 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. + + </help> + <citations> + <citation type="doi">https://doi.org/10.1101/050559</citation> + </citations> +</tool>
--- /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 @@ +<data_managers> + <data_manager tool_file="data_manager/malt_index_builder.xml" id="data_manager_malt_index_builder"> + <data_table name="malt_indices"> + <output> + <column name="value"/> + <column name="dbkey"/> + <column name="name"/> + <column name="path" output_ref="out_file"> + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">malt_index/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/malt_index/${value}</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/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): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#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
--- /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
--- /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
--- /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 +
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#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. +#
--- /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): +# +# <unique_build_id> <dbkey> <display_name> <directory_path> +# +# 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
--- /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 @@ +<tables> + <!-- Locations of indices MALT versions 0.5.3 and higher --> + <table name="malt_indices" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/malt_indices.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Nov 17 08:22:56 2021 +0000 @@ -0,0 +1,12 @@ +<tables> + <!-- Location of index files for malt_build version 0.5.3 and higher --> + <table name="malt_indices" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/malt_indices.loc" /> + </table> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables>