Mercurial > repos > sanbi-uwc > data_manager_primer_scheme_bedfiles
changeset 0:00ed379c9df1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 88130bb7c37cca7eff6df235ba17e0ae9f11df86-dirty"
| author | sanbi-uwc |
|---|---|
| date | Sat, 18 Apr 2020 15:21:47 +0000 |
| parents | |
| children | 193e5a407be8 |
| files | data_manager/install_primer_scheme_bedfiles.py data_manager/install_primer_scheme_bedfiles.xml data_manager/test.json data_manager/tmp/ARTICv1.bed data_manager/tmp/test.bed data_manager_conf.xml tool-data/artic_sars_cov2_primers.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 8 files changed, 405 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/install_primer_scheme_bedfiles.py Sat Apr 18 15:21:47 2020 +0000 @@ -0,0 +1,122 @@ +#!/usr/bin/env python + +from __future__ import print_function, division + +import argparse +import json +import os +import os.path +import re +import sys +import shutil + +import requests + +DATA_TABLE_NAME = "primer_scheme_bedfiles" + + +def fetch_artic_primers(output_directory, primers): + primer_sets = { + "ARTICv1": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed", + "ARTICv2": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed", + "ARTICv3": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed", + } + + data = [] + for name, url in primer_sets.items(): + if name not in primers: + continue + response = requests.get(url) + if response.status_code != 200: + print( + "Error: download of", + url, + "failed with code", + response.status_code, + file=sys.stderr, + ) + exit(response.status_code) + bed_output_filename = os.path.join(output_directory, name + ".bed") + open(bed_output_filename, "w").write(response.text) + description = name[:-2] + " " + name[-2:] + " primer set" + data.append(dict(value=name, path=bed_output_filename, description=description)) + return data + + +def install_primer_file(output_directory, input_filename, primer_name, primer_description): + name = re.sub(r'\W', '', str(primer_name).replace(' ','_')) + output_filename = os.path.join(output_directory, name + '.bed') + shutil.copyfile(input_filename, output_filename) + data = [dict(value=name, description=primer_description, path=output_filename)] + return data + +class SplitArgs(argparse.Action): + def __call__(self, parser, namespace, values, option_string=None): + setattr(namespace, self.dest, values.split(",")) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + description="Fetch ARTIC SARS-CoV-2 primer files for Galaxy/IRIDA use" + ) + parser.add_argument( + "--output_directory", default="tmp", help="Directory to write output to" + ) + primer_file = parser.add_argument_group() + primer_file.add_argument( + "--primer_file", help="BED format file containing primer scheme" + ) + primer_file.add_argument( + "--primer_name", help="Name of primer scheme (one word). Required if --primer_file is used" + ) + primer_file.add_argument( + "--primer_description", help="Description of primer scheme. Required if --primer_file is used" + ) + artic = parser.add_argument_group() + artic.add_argument( + "--primers", + action=SplitArgs, + help="Comma separated list of primers to fetch", + ) + parser.add_argument( + "galaxy_datamanager_filename", + help="Galaxy JSON format file describing data manager inputs", + ) + args = parser.parse_args() + + if args.primers is None and args.primer_file is None: + print("One of --primers or --primer_file + --primer_name + --primer_description is required.", file=sys.stderr) + exit(1) + elif args.primer_file is not None and (args.primer_name is None or args.primer_description is None): + print("If --primer_file is used --primer_name and --primer_description is also required", file=sys.stderr) + exit(1) + elif args.primer_file is not None and args.primers is not None: + print("Only one of --primers or --primer_file + --primer_name + --primer_description can be chosen") + exit(1) + + config = json.load(open(args.galaxy_datamanager_filename)) + output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None) + if output_directory is None: + output_directory = args.output_directory + + if not os.path.isdir(output_directory): + os.makedirs(output_directory) + + data_manager_dict = {} + data_manager_dict["data_tables"] = json.load(open(args.galaxy_datamanager_filename)).get( + "data_tables", {} + ) + 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, []) + + if args.primers: + data = fetch_artic_primers(output_directory, args.primers) + else: + data = install_primer_file(output_directory, args.primer_file, args.primer_name, args.primer_description) + + data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data) + print(data_manager_dict) + json.dump(data_manager_dict, open(args.galaxy_datamanager_filename, "w")) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/install_primer_scheme_bedfiles.xml Sat Apr 18 15:21:47 2020 +0000 @@ -0,0 +1,51 @@ +<tool id="data_manager_primer_scheme_bedfiles" name="ARTIC SARS-CoV-2 primer data manager" version="0.0.1" tool_type="manage_data" profile="19.05"> + <requirements> + <requirement type="package">python</requirement> + <requirement type="package" version="2.22.0">requests</requirement> + </requirements> + <!-- fetch all the primers in one go --> + <command detect_errors="exit_code"> + python '$__tool_directory__/fetch_artic_sars_cov2_primers.py' + '${output_file}' + #if $input.input_type == "ARTIC" + --artic_primers '${primers}' + #else + --primer_file '${input.primer_input}' + --primer_name '${input.primer_name}' + --primer_description '${input.primer_description}' + </command> + <inputs> + <conditional name="input"> + <param name="input_type" label="Choose the source for primer schemes" type="select"> + <option value="ARTIC" selected="true">ARTIC Github page</option> + <option value="history">History</option> + </param> + <when value="ARTIC"> + <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch"> + <option value="ARTICv1" selected="true">ARTIC v1</option> + <option value="ARTICv2" selected="true">ARTIC v2</option> + <option value="ARTICv3" selected="true">ARTIC v3</option> + </param> + </when> + <when value="history"> + <param name="primer_input" label="Select history item" type="data" format="bed" /> + <param name="primer_name" label="Name for this primer scheme" type="text" + help="Non-word characters will be removed from primer scheme name and spaces replaced with underscore (_)" /> + <param name="primer_description" label="Description for primer scheme" type="text" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_file" format="data_manager_json"/> + </outputs> + <tests> + <test> + <param name="primers" value="ARTICv1,ARTICv2,ARTICv3"/> + <output name="output_file"> + <assert_contents> + <has_text text="ARTIC"/> + </assert_contents> + </output> + </test> + </tests> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/test.json Sat Apr 18 15:21:47 2020 +0000 @@ -0,0 +1,1 @@ +{"data_tables": {"primer_scheme_bedfiles": [{"value": "test", "description": "test", "path": "tmp/test.bed"}, {"value": "ARTICv1", "path": "tmp/ARTICv1.bed", "description": "ARTIC v1 primer set"}]}} \ No newline at end of file
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/tmp/test.bed Sat Apr 18 15:21:47 2020 +0000 @@ -0,0 +1,1 @@ +{}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Sat Apr 18 15:21:47 2020 +0000 @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/install_primer_scheme_bedfiles.xml" id="data_manager_primer_scheme_bedfiles"> + <data_table name="primer_scheme_bedfiles"> + <output> + <column name="value" /> + <column name="description" /> + <column name="path" output_ref="output_file" > + <!-- note: the Python script sanitises the possibly user-supplied scheme name ('value') --> + <move type="file"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">primer_scheme_bedfiles/#echo str($value)#.bed</target> + </move> + <value_translation>primer_scheme_bedfiles/#echo str($value)#.bed</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/tool-data/artic_sars_cov2_primers.loc.sample Sat Apr 18 15:21:47 2020 +0000 @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of ARTIC primers for use in SARS-CoV-2 sequencing +# +# the columns are: +# value description path +# +# for example +# ARTICv1 ARTIC v1 primers /data/galaxy/tool_data/artic_primers/ARTICv1.bed \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Apr 18 15:21:47 2020 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of primer scheme BED files --> + <table name="primer_scheme_bedfiles" comment_char="#"> + <columns>value, description, path</columns> + <file path="tool-data/primer_scheme_bedfiles.loc" /> + </table> +</tables>