Mercurial > repos > iuc > data_manager_bowtie_index_builder
changeset 8:9c91b5015dd3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
| author | iuc |
|---|---|
| date | Thu, 05 Dec 2024 06:49:01 +0000 |
| parents | 39a922d01b0d |
| children | |
| files | data_manager/bowtie_color_space_index_builder.xml data_manager/bowtie_index_builder.py data_manager/bowtie_index_builder.xml data_manager_conf.xml test-data/all_fasta.loc test-data/bowtie_data_manager.1.json test-data/bowtie_data_manager.2.json test-data/bowtie_indices.loc test-data/phiX174.fasta tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 10 files changed, 180 insertions(+), 167 deletions(-) [+] |
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--- a/data_manager/bowtie_color_space_index_builder.xml Tue May 21 07:35:37 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -<tool id="bowtie_color_space_index_builder_data_manager" name="Bowtie Color index" tool_type="manage_data" version="1.2.1" profile="23.0"> - <description>builder</description> - <requirements> - <requirement type="package" version="1.2.0">bowtie</requirement> - <requirement type="package" version="3.8.3">python</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ -python '$__tool_directory__/bowtie_index_builder.py' -'${out_file}' ---fasta_filename '${all_fasta_source.fields.path}' ---fasta_dbkey '${all_fasta_source.fields.dbkey}' ---fasta_description '${all_fasta_source.fields.name}' ---data_table_name bowtie_indexes_color ---color_space - ]]></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" help="Leave blank to use all_fasta name" /> - <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" /> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json"/> - </outputs> - <help><![CDATA[ -.. class:: infomark - -**Notice:** If you leave name, description, or id blank, it will be generated automatically. - ]]></help> - <citations> - <citation type="doi">10.1186/gb-2009-10-3-r25</citation> - </citations> -</tool>
--- a/data_manager/bowtie_index_builder.py Tue May 21 07:35:37 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ -#!/usr/bin/env python -from __future__ import print_function - -import json -import optparse -import os -import subprocess -import sys -import tempfile - -CHUNK_SIZE = 2**20 - -DEFAULT_DATA_TABLE_NAME = "bowtie_indexes" - - -def get_id_name(params, dbkey, fasta_description=None): - # TODO: ensure sequence_id is unique and does not already appear in location file - 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_bowtie_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME, color_space=False): - # TODO: allow multiple FASTA input files - 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 = ['bowtie-build'] - if color_space: - args.append('-C') - args.append(sym_linked_fasta_filename) - args.append(fasta_base_name) - args.append(sym_linked_fasta_filename) - tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-bowtie-index-builder-stderr") - proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno()) - return_code = proc.wait() - if return_code: - tmp_stderr.flush() - tmp_stderr.seek(0) - print("Error building index:", file=sys.stderr) - while True: - chunk = tmp_stderr.read(CHUNK_SIZE) - if not chunk: - break - sys.stderr.write(chunk) - sys.exit(return_code) - tmp_stderr.close() - data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name) - _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) - - -def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): - 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", default=None, help='fasta_filename') - parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey') - parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description') - parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name') - parser.add_option('-c', '--color_space', dest='color_space', action='store_true', default=False, help='color_space') - (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_bowtie_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME, color_space=options.color_space) - - # save info to json file - with open(filename, 'w') as fh: - json.dump(data_manager_dict, fh, sort_keys=True) - - -if __name__ == "__main__": - main()
--- a/data_manager/bowtie_index_builder.xml Tue May 21 07:35:37 2024 +0000 +++ b/data_manager/bowtie_index_builder.xml Thu Dec 05 06:49:01 2024 +0000 @@ -1,17 +1,39 @@ -<tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="1.2.1" profile="23.0"> +<tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> <description>builder</description> + <macros> + <token name="@WRAPPER_VERSION@">1.3.1</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> <requirements> - <requirement type="package" version="1.2.0">bowtie</requirement> - <requirement type="package" version="3.8.3">python</requirement> + <requirement type="package" version="@WRAPPER_VERSION@">bowtie</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ -python '$__tool_directory__/bowtie_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}' ---data_table_name bowtie_indexes - ]]></command> + #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] + mkdir -p '${out_file.extra_files_path}' && + ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' && + bowtie-build '${out_file.extra_files_path}/${fasta_file_name}' '${out_file.extra_files_path}/${fasta_file_name}' && + cp '$dmjson' '$out_file' + ]]> + </command> + <configfiles> + <configfile name="dmjson"><![CDATA[#slurp +#set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] +#set $value = $sequence_id or $all_fasta_source.fields.dbkey +#set $name = $sequence_name or $all_fasta_source.fields.name +{ + "data_tables":{ + "bowtie_indexes":[ + { + "value": "${value}", + "dbkey": "${all_fasta_source.fields.dbkey}", + "name": "${name}", + "path": "${fasta_file_name}" + } + ] + } +} +]]></configfile> + </configfiles> <inputs> <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> <options from_data_table="all_fasta"/> @@ -22,6 +44,18 @@ <outputs> <data name="out_file" format="data_manager_json"/> </outputs> + <tests> + <test> + <param name="all_fasta_source" value="phiX174"/> + <output name="out_file" file="bowtie_data_manager.1.json"/> + </test> + <test> + <param name="all_fasta_source" value="phiX174"/> + <param name="sequence_name" value="Galeocerdo cuvier"/> + <param name="sequence_id" value="tigHai1"/> + <output name="out_file" file="bowtie_data_manager.2.json"/> + </test> + </tests> <help><![CDATA[ .. class:: infomark
--- a/data_manager_conf.xml Tue May 21 07:35:37 2024 +0000 +++ b/data_manager_conf.xml Thu Dec 05 06:49:01 2024 +0000 @@ -9,26 +9,9 @@ <column name="path" output_ref="out_file" > <move type="directory" relativize_symlinks="True"> <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/bowtie_index</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/bowtie_index/v1/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie_index/${path}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - </output> - </data_table> - </data_manager> - <data_manager tool_file="data_manager/bowtie_color_space_index_builder.xml" id="bowtie_color_space_index_builder"> - <data_table name="bowtie_indexes_color"> - <output> - <column name="value" /> - <column name="dbkey" /> - <column name="name" /> - <column name="path" output_ref="out_file" > - <move type="directory" relativize_symlinks="True"> - <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/bowtie_index/color</target> <!-- confirm this as preferred location --> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie_index/color/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v1/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Thu Dec 05 06:49:01 2024 +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 phiX 174 ${__HERE__}/phiX174.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_data_manager.1.json Thu Dec 05 06:49:01 2024 +0000 @@ -0,0 +1,12 @@ +{ + "data_tables":{ + "bowtie_indexes":[ + { + "value": "phiX174", + "dbkey": "phiX174", + "name": "phiX 174", + "path": "phiX174.fasta" + } + ] + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_data_manager.2.json Thu Dec 05 06:49:01 2024 +0000 @@ -0,0 +1,12 @@ +{ + "data_tables":{ + "bowtie_indexes":[ + { + "value": "tigHai1", + "dbkey": "phiX174", + "name": "Galeocerdo cuvier", + "path": "phiX174.fasta" + } + ] + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Thu Dec 05 06:49:01 2024 +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 +
--- a/tool_data_table_conf.xml.sample Tue May 21 07:35:37 2024 +0000 +++ b/tool_data_table_conf.xml.sample Thu Dec 05 06:49:01 2024 +0000 @@ -9,9 +9,4 @@ <columns>value, dbkey, name, path</columns> <file path="tool-data/bowtie_indices.loc" /> </table> - <!-- Locations of indexes in the Bowtie color-space mapper format --> - <table name="bowtie_indexes_color" comment_char="#" allow_duplicate_entries="False"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/bowtie_indices_color.loc" /> - </table> </tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Dec 05 06:49:01 2024 +0000 @@ -0,0 +1,12 @@ +<tables> + <!-- 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> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="bowtie_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/bowtie_indices.loc" /> + </table> +</tables>