| Previous changeset 0:1d9e3950ce61 (2017-12-20) Next changeset 2:d465e81782a3 (2018-03-24) |
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Commit message:
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 83ebe793451a5ccbfeff873eda359f699e14ae1e |
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modified:
data_managers/data_manager_conf.xml data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml tools/mentalist_call/mentalist_call.xml |
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added:
data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml data_managers/data_manager_mentalist_download_enterobase/tool_data_table_conf.xml.sample |
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| diff -r 1d9e3950ce61 -r c6a98b93e569 data_managers/data_manager_conf.xml --- a/data_managers/data_manager_conf.xml Wed Dec 20 17:36:03 2017 -0500 +++ b/data_managers/data_manager_conf.xml Sat Mar 24 23:12:21 2018 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.3"> + <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.2.2"> <data_table name="mentalist_databases"> <output> <column name="value" /> @@ -15,7 +15,7 @@ </output> </data_table> </data_manager> - <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.3"> + <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.2.2"> <data_table name="mentalist_databases"> <output> <column name="value" /> @@ -30,7 +30,22 @@ </output> </data_table> </data_manager> - <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.3"> + <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.2.2"> + <data_table name="mentalist_databases"> + <output> + <column name="value" /> + <column name="name" /> + <column name="path" output_ref="out_file"> + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> + <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="0.2.2"> <data_table name="mentalist_databases"> <output> <column name="value" /> |
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| diff -r 1d9e3950ce61 -r c6a98b93e569 data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml --- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml Wed Dec 20 17:36:03 2017 -0500 +++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml Sat Mar 24 23:12:21 2018 -0400 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.3"> +<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.2.2"> <requirements> - <requirement type="package" version="0.1.3">mentalist</requirement> + <requirement type="package" version="0.2.2">mentalist</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ @@ -31,5 +31,6 @@ </outputs> <citations> <citation type="doi">10.1101/172858</citation> + <citation type="doi">10.1099/mgen.0.000146</citation> </citations> </tool> |
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| diff -r 1d9e3950ce61 -r c6a98b93e569 data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml --- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml Wed Dec 20 17:36:03 2017 -0500 +++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml Sat Mar 24 23:12:21 2018 -0400 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.3"> +<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.2.2"> <requirements> - <requirement type="package" version="0.1.3">mentalist</requirement> + <requirement type="package" version="0.2.2">mentalist</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ @@ -20,6 +20,8 @@ <option value="Clostridioides difficile">Clostridioides difficile</option> <option value="Enterococcus faecium">Enterococcus faecium</option> <option value="Francisella tularensis">Francisella tularensis</option> + <option value="Klebsiella pneumoniae/variicola/quasipneumoniae">Klebsiella pneumoniae/variicola/quasipneumoniae</option> + <option value="Mycobacterium tuberculosis/bovis/africanum/canettii">Mycobacterium tuberculosis/bovis/africanum/canettii</option> <option value="Legionella pneumophila">Legionella pneumophila</option> <option value="Listeria monocytogenes">Listeria monocytogenes</option> <option value="Staphylococcus aureus">Staphylococcus aureus</option> @@ -30,5 +32,6 @@ </outputs> <citations> <citation type="doi">10.1101/172858</citation> + <citation type="doi">10.1099/mgen.0.000146</citation> </citations> </tool> |
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| diff -r 1d9e3950ce61 -r c6a98b93e569 data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py Sat Mar 24 23:12:21 2018 -0400 |
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| @@ -0,0 +1,74 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import datetime +import errno +import os +import string +import subprocess +import sys + +from json import dumps, loads + + +DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"] + + +def mentalist_download_enterobase( data_manager_dict, kmer_size, scheme, type, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): + translation_table = string.maketrans(string.punctuation, ("_" * 32)) + base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_enterobase" + today = datetime.date.today().isoformat() + scheme_files_path = base_path + "_scheme_" + today + database_path = base_path + "_k" + str(kmer_size) + "_" + today + database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld" + display_name = scheme + " k=" + str(kmer_size) + " (Enterobase) " + today + args = [ 'mentalist', 'download_enterobase', '-s', scheme, '-t', type, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path] + proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) + return_code = proc.wait() + if return_code: + print("Error building database.", file=sys.stderr) + sys.exit( return_code ) + data_table_entry = dict( value=database_path, dbkey='Enterobase', name=display_name, path=database_name ) + for data_table_name in data_table_names: + _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 = argparse.ArgumentParser() + parser.add_argument('params') + parser.add_argument( '-s', '--scheme', dest='scheme', default=None, help="Scheme: ('E'=Escherichia/Shigella, 'S'=Salmonella, 'Y'=Yersinia)") + parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' ) + parser.add_argument( '-t', '--type', dest='type', default=None, help="Type: ('cg'=cgMLST, 'wg'=wgMLST')") + args = parser.parse_args() + + params = loads( open( args.params ).read() ) + target_directory = params[ 'output_data' ][0]['extra_files_path'] + + try: + os.mkdir( target_directory ) + except OSError as exc: + if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): + pass + else: + raise + + data_manager_dict = {} + + # build the index + mentalist_download_enterobase( data_manager_dict, args.kmer_size, args.scheme, args.type, params, target_directory, DEFAULT_DATA_TABLE_NAMES ) + + # save info to json file + open( args.params, 'wb' ).write( dumps( data_manager_dict ) ) + + +if __name__ == "__main__": + main() |
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| diff -r 1d9e3950ce61 -r c6a98b93e569 data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml Sat Mar 24 23:12:21 2018 -0400 |
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| @@ -0,0 +1,35 @@ +<?xml version="1.0"?> +<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.2.2"> + <requirements> + <requirement type="package" version="0.2.2">mentalist</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/mentalist_download_enterobase.py' + '${out_file}' + -k '$kmer_size' + --scheme '$scheme' + --type '$type' + ]]> + </command> + <inputs> + <param name="kmer_size" type="integer" + label="Kmer size" help="Kmer size" + value="31" min="1" max="32" /> + <param name="scheme" type="select" multiple="false" label="Select scheme to download"> + <option value="E">Escherichia/Shigella</option> + <option value="S">Salmonella</option> + <option value="Y">Yersinia</option> + </param> + <param name="type" type="select" multiple="false" label="Select scheme type (cgMLST or wgMLST)"> + <option value="cg">Core Genome (cgMLST)</option> + <option value="wg">Whole Genome (wgMLST)</option> + </param> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <citations> + <citation type="doi">10.1101/172858</citation> + </citations> +</tool> |
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| diff -r 1d9e3950ce61 -r c6a98b93e569 data_managers/data_manager_mentalist_download_enterobase/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_managers/data_manager_mentalist_download_enterobase/tool_data_table_conf.xml.sample Sat Mar 24 23:12:21 2018 -0400 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!--Locations of MentaLiST database in the required format --> + <table name="mentalist_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/mentalist_databases.loc" /> + </table> +</tables> \ No newline at end of file |
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| diff -r 1d9e3950ce61 -r c6a98b93e569 data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml --- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml Wed Dec 20 17:36:03 2017 -0500 +++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml Sat Mar 24 23:12:21 2018 -0400 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.3"> +<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.2.2"> <requirements> - <requirement type="package" version="0.1.3">mentalist</requirement> + <requirement type="package" version="0.2.2">mentalist</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ @@ -76,6 +76,7 @@ <option value="Helicobacter pylori">Helicobacter pylori</option> <option value="Helicobacter suis">Helicobacter suis</option> <option value="Kingella kingae">Kingella kingae</option> + <option value="Klebsiella aerogenes">Klebsiella aerogenes</option> <option value="Klebsiella oxytoca">Klebsiella oxytoca</option> <option value="Klebsiella pneumoniae">Klebsiella pneumoniae</option> <option value="Kudoa septempunctata">Kudoa septempunctata</option> @@ -155,5 +156,6 @@ </outputs> <citations> <citation type="doi">10.1101/172858</citation> + <citation type="doi">10.1099/mgen.0.000146</citation> </citations> </tool> |
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| diff -r 1d9e3950ce61 -r c6a98b93e569 tools/mentalist_call/mentalist_call.xml --- a/tools/mentalist_call/mentalist_call.xml Wed Dec 20 17:36:03 2017 -0500 +++ b/tools/mentalist_call/mentalist_call.xml Sat Mar 24 23:12:21 2018 -0400 |
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| @@ -1,16 +1,23 @@ -<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.3"> +<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.2.2"> <requirements> - <requirement type="package" version="0.1.3">mentalist</requirement> + <requirement type="package" version="0.2.2">mentalist</requirement> </requirements> + <edam_operations> + <edam_operation>operation_3840</edam_operation> + </edam_operations> <command detect_errors="exit_code"><![CDATA[ mentalist call -o '$output_file' --db '$kmer_db.fields.path' + --mutation_threshold '$mutation_threshold' + --kt '$kmer_threshold' + $output_votes + $output_special #if $input_type.sPaired == "paired": - -s $input_type.pInput1.name $input_type.pInput1 $input_type.pInput2 + -s $input_type.pInput1.name -1 $input_type.pInput1 -2 $input_type.pInput2 #elif $input_type.sPaired == "collections": - -s $input_type.fastq_collection.name $input_type.fastq_collection.forward $input_type.fastq_collection.reverse + -s $input_type.fastq_collection.name -1 $input_type.fastq_collection.forward -2 $input_type.fastq_collection.reverse #end if ]]></command> <inputs> @@ -32,13 +39,27 @@ <validator type="no_options" message="No MentaLiST databases are available" /> </options> </param> + <param name="mutation_threshold" type="integer" label="Mutation threshold" + help="Maximum number of mutations when looking for novel alleles." + value="6" min="1" max="25" /> + <param name="kmer_threshold" type="integer" label="Kmer threshold" + help="Minimum number of times a kmer is seen to be considered present in the sample." + value="10" min="1" max="25" /> + <param name="output_votes" type="boolean" label="Output votes" + argument="--output_votes" truevalue="--output_votes" falsevalue="" + help="Outputs the results for the original voting algorithm" /> + <param name="output_special" type="boolean" label="Output special" + argument="--output_special" truevalue="--output_special" falsevalue="" + help="Outputs a fasta file with the alleles from special cases such as incomplete coverage, novel and multiple alleles." /> </inputs> <outputs> - <data name="output_file" format="tabular"/> + <data name="output_file" format="tabular" /> + <data name="coverage_file" format="tabular" /> </outputs> <help><![CDATA[ ]]></help> <citations> <citation type="doi">10.1101/172858</citation> + <citation type="doi">10.1099/mgen.0.000146</citation> </citations> </tool> |