Mercurial > repos > iuc > data_manager_homer_preparse
changeset 0:e6a2110ac3b9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
| author | iuc |
|---|---|
| date | Sun, 08 Aug 2021 11:01:47 +0000 |
| parents | |
| children | d9c177013aba |
| files | data_manager/homer_genome_preparse.py data_manager/homer_genome_preparse.xml data_manager_conf.xml test-data/all_fasta.loc test-data/homer_preparse.loc test-data/phiX174.fasta tool-data/all_fasta.loc.sample tool-data/homer_preparse.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 10 files changed, 367 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/homer_genome_preparse.py Sun Aug 08 11:01:47 2021 +0000 @@ -0,0 +1,94 @@ +#!/usr/bin/env python +# Dan Blankenberg for bowtie2 +# Modified by Lucille Delisle for homer +from __future__ import print_function + +import json +import optparse +import os +import subprocess +import sys + +DEFAULT_DATA_TABLE_NAME = "homer_preparse" + + +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 homer_preparse(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, + sequence_name, size, mask, version, + data_table_name=DEFAULT_DATA_TABLE_NAME): + args = ['preparseGenome.pl', fasta_filename, '-size', str(size), '-preparsedDir', target_directory] + if mask: + args.append('-mask') + proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) + return_code = proc.wait() + if return_code: + print("Error preparsing genome.", file=sys.stderr) + sys.exit(return_code) + mask_suffix = 'r' if mask else '' + mask_suffix_name = ' masked' if mask else '' + data_table_entry = dict(value=sequence_id + mask_suffix + '_' + str(size), dbkey=dbkey, + mask=str(mask), size=str(size), name=sequence_name + mask_suffix_name + ' (' + str(size) + 'bp)', + path=sequence_id + mask_suffix + '_' + str(size), + path_fasta=fasta_filename, + version=version) + _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('-s', '--size', dest='size', action='store', type="int", default=200, help='fragment size') + parser.add_option('-m', '--mask', dest='mask', action='store_true', default=False, help='mask the lower case bases (repeats)') + parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name') + parser.add_option('--index_version', dest='index_version', action='store', type="string", default=None, help='index version') + (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) + + # preparse the genome + homer_preparse(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, + sequence_name, options.size, options.mask, options.index_version, + data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME) + + # 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/homer_genome_preparse.xml Sun Aug 08 11:01:47 2021 +0000 @@ -0,0 +1,60 @@ +<tool id="homer_genome_preparse_data_manager" name="Homer genome preparse" tool_type="manage_data" version="@IDX_VERSION@" profile="20.05"> + <requirements> + <requirement type="package" version="@IDX_VERSION@">homer</requirement> + <requirement type="package" version="3.9">python</requirement> + </requirements> + <macros> + <token name="@IDX_VERSION@">4.11</token> + </macros> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/homer_genome_preparse.py' + '${out_file}' + --fasta_filename '${all_fasta_source.fields.path}' + --fasta_dbkey '${all_fasta_source.fields.dbkey}' + --fasta_description '${all_fasta_source.fields.name}' + ${mask} + --size '${size}' + --index_version '@IDX_VERSION@' + --data_table_name homer_preparse + ]]></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="mask" type="boolean" truevalue="--mask" falsevalue="" checked="False" label="mask repeats/lower case sequence" /> + <param name="size" type="integer" value="200" min="0" label="fragment size to use for motif finding" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <tests> + <test> + <param name="all_fasta_source" value="phiX174"/> + <output name="out_file" > + <assert_contents> + <has_text text="{"data_tables": {"homer_preparse": [{"dbkey": "phiX174", "mask": "False", "name": "phiX174 (200bp)", "path": "phiX174_200", "path_fasta":" /> + <has_text text="test-data/phiX174.fasta", "size": "200", "value": "phiX174_200", "version": "4.11"}]}}" /> + </assert_contents> + </output> + </test> + <test> + <param name="all_fasta_source" value="phiX174"/> + <param name="mask" value="True"/> + <param name="size" value="100"/> + <output name="out_file" > + <assert_contents> + <has_text text="{"data_tables": {"homer_preparse": [{"dbkey": "phiX174", "mask": "True", "name": "phiX174 masked (100bp)", "path": "phiX174r_100", "path_fasta":" /> + <has_text text="test-data/phiX174.fasta", "size": "100", "value": "phiX174r_100", "version": "4.11"}]}}" /> + </assert_contents> + </output> + </test> + </tests> + + <help> +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Sun Aug 08 11:01:47 2021 +0000 @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/homer_genome_preparse.xml" id="homer_genome_preparse" version="4.11"> + <data_table name="homer_preparse"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="mask" /> + <column name="size" /> + <column name="name" /> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/homer_preparse/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/homer_preparse/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + <column name="path_fasta"/> + <column name="version" /> + </output> + </data_table> + </data_manager> +</data_managers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Sun Aug 08 11:01:47 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/homer_preparse.loc Sun Aug 08 11:01:47 2021 +0000 @@ -0,0 +1,25 @@ +# homer_preparse.loc +# This is a *.loc file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Homer preparsed genomes. +# The file should include an one line entry for each index set. +# The path points to the "directory" for the set, not a specific file. +# It has six text columns seperated by TABS. +# +# <unique_preparse_id> <dbkey> <mask> <size> <display_name> <directory_path> <path_fasta> <version> +# +# So, for example, if you had phiX174 preparsed with 200bp stored in: +# +# /tmp/phix_200 +# +# containing phiX174.fasta.200.* files, such as: +# -rw-r--r-- 1 ldelisle ldelisle 83K Jul 9 10:14 phiX174.fasta.200.cgbins +# -rw-r--r-- 1 ldelisle ldelisle 249K Jul 9 10:14 phiX174.fasta.200.cgfreq +# -rw-r--r-- 1 ldelisle ldelisle 83K Jul 9 10:14 phiX174.fasta.200.gcbins +# -rw-r--r-- 1 ldelisle ldelisle 169K Jul 9 10:14 phiX174.fasta.200.pos +# -rw-r--r-- 1 ldelisle ldelisle 955K Jul 9 10:14 phiX174.fasta.200.seq +# +# then the homer_preparse.loc entry could look like this: +# +# phiX174_200 phiX174 False 200 phiX174 (200bp) /tmp/phix_200 /tmp/phiX174.fasta 4.11 +# +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Sun Aug 08 11:01:47 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 Sun Aug 08 11:01:47 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/homer_preparse.loc.sample Sun Aug 08 11:01:47 2021 +0000 @@ -0,0 +1,25 @@ +# homer_preparse.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Homer preparsed genomes. +# The file should include an one line entry for each index set. +# The path points to the "directory" for the set, not a specific file. +# It has six text columns seperated by TABS. +# +# <unique_preparse_id> <dbkey> <mask> <size> <display_name> <directory_path> <path_fasta> <version> +# +# So, for example, if you had phiX174 preparsed with 200bp stored in: +# +# /tmp/phix_200 +# +# containing phiX174.fasta.200.* files, such as: +# -rw-r--r-- 1 ldelisle ldelisle 83K Jul 9 10:14 phiX174.fasta.200.cgbins +# -rw-r--r-- 1 ldelisle ldelisle 249K Jul 9 10:14 phiX174.fasta.200.cgfreq +# -rw-r--r-- 1 ldelisle ldelisle 83K Jul 9 10:14 phiX174.fasta.200.gcbins +# -rw-r--r-- 1 ldelisle ldelisle 169K Jul 9 10:14 phiX174.fasta.200.pos +# -rw-r--r-- 1 ldelisle ldelisle 955K Jul 9 10:14 phiX174.fasta.200.seq +# +# then the homer_preparse.loc entry could look like this: +# +# phiX174_200 phiX174 False 200 phiX174 (200bp) /tmp/phix_200 /tmp/phiX174.fasta 4.11 +# +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Aug 08 11:01:47 2021 +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="tool-data/all_fasta.loc" /> + </table> + <!-- Locations of preparsed genomes --> + <table name="homer_preparse" comment_char="#"> + <columns>value, dbkey, mask, size, name, path, path_fasta, version</columns> + <file path="tool-data/homer_preparse.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sun Aug 08 11:01:47 2021 +0000 @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of preparsed genomes when running tests--> + <table name="homer_preparse" comment_char="#"> + <columns>value, dbkey, mask, size, name, path, path_fasta, version</columns> + <file path="${__HERE__}/test-data/homer_preparse.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>