| Previous changeset 0:e1502e4f8725 (2024-02-21) Next changeset 2:f8d72275878e (2024-08-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 67067cd7917545904b3a9980948abdd19f0576bd |
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modified:
data_manager/macros.xml data_manager/omamer.py data_manager/omamer.xml data_manager_conf.xml |
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added:
test-data/out.json |
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removed:
data_manager/test.json test-data/omamer.loc tool_data_table_conf.xml.test |
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| diff -r e1502e4f8725 -r 57db282ca204 data_manager/macros.xml --- a/data_manager/macros.xml Wed Feb 21 19:26:53 2024 +0000 +++ b/data_manager/macros.xml Thu Mar 07 14:28:42 2024 +0000 |
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| @@ -1,8 +1,12 @@ + <macros> + <token name="@TOOL_VERSION@">2.0.2</token> + <token name="@VERSION_SUFFIX@">1</token> + <xml name="requirements"> <requirements> <requirement type="package" version="3.11">python</requirement> <requirement type="package" version="2.27.1">requests</requirement> </requirements> </xml> -</macros> \ No newline at end of file +</macros> |
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| diff -r e1502e4f8725 -r 57db282ca204 data_manager/omamer.py --- a/data_manager/omamer.py Wed Feb 21 19:26:53 2024 +0000 +++ b/data_manager/omamer.py Thu Mar 07 14:28:42 2024 +0000 |
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| @@ -4,7 +4,6 @@ import json import os import sys -from pathlib import Path import requests @@ -19,7 +18,6 @@ "LUCA": "LUCA-v0.2.5.h5", } - DEFAULT_OUTPUT_DIR = "database_omamer" @@ -37,12 +35,14 @@ def main(args): - # Set output directory to default - output_dir = DEFAULT_OUTPUT_DIR + + with open(args.json) as fh: + params = json.load(fh) + target_directory = params["output_data"][0]["extra_files_path"] # Create output directory if none exists - if not os.path.exists(output_dir): - os.makedirs(output_dir) + if not os.path.exists(target_directory): + os.makedirs(target_directory) # Check if the selected dataset exists if args.name not in OMAMER_DATASETS: @@ -53,18 +53,18 @@ dataset = OMAMER_DATASETS[args.name] url = OMAMER_DATASETS_URL.format(dataset=dataset) base_name = os.path.splitext(dataset)[0] - destination_path = os.path.join(output_dir, base_name) + destination_path = os.path.join(target_directory, dataset) download_file(url, destination_path) data_manager_entry = { - "value": os.path.splitext(os.path.basename(base_name))[0], - "name": os.path.splitext(os.path.basename(base_name))[0], - "version": "2.0.2", - "path": str(Path(output_dir)), + "value": dataset, + "name": base_name, + "version": args.version, + "path": dataset, } # Creates a JSON dictionary representing the Data Manager configuration - data_manager_json = {"data_tables": {"omamer_data": [data_manager_entry]}} + data_manager_json = {"data_tables": {"omamer": [data_manager_entry]}} # Writes this JSON dictionary to the specified output file with open(args.json, "w") as fh: @@ -76,6 +76,7 @@ parser = argparse.ArgumentParser(description='Download data for OMAmer') parser.add_argument('--name', default='Primates', choices=OMAMER_DATASETS.keys(), help='Select dataset to download') parser.add_argument('--json', help='Path to JSON file') + parser.add_argument("--version", help="Omamer version") args = parser.parse_args() |
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| diff -r e1502e4f8725 -r 57db282ca204 data_manager/omamer.xml --- a/data_manager/omamer.xml Wed Feb 21 19:26:53 2024 +0000 +++ b/data_manager/omamer.xml Thu Mar 07 14:28:42 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="data_manager_omamer" name="OMAmer data manager" version="2.0.2" tool_type="manage_data" profile="20.01"> +<tool id="data_manager_omamer" name="OMAmer data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01"> <macros> <import>macros.xml</import> </macros> @@ -7,6 +7,7 @@ python '$__tool_directory__/omamer.py' --name '$name' --json '$output_file' + --version '@TOOL_VERSION@' ]]></command> <inputs> <param name="output_dir" type="text" label="Output Directory" value=""/> @@ -17,7 +18,7 @@ <option value="LUCA">LUCA</option> </param> </inputs> - + <outputs> <data name="output_file" format="data_manager_json" label="OMAmer data manager: JSON"/> </outputs> @@ -26,15 +27,10 @@ <test> <param name="output_dir" value="test_galaxy"/> <param name="name" value="Primates"/> - <output name="output_file"> - <assert_contents> - <has_text text="Primates-v2.0"/> - <has_text text="database_omamer"/> - </assert_contents> - </output> + <output name="output_file" file="out.json"/> </test> </tests> - + <help><![CDATA[ This data manager retrieves data from various pre-built databases. @@ -43,4 +39,4 @@ <citations> <citation type="doi">10.1093/bioinformatics/btab219</citation> </citations> -</tool> \ No newline at end of file +</tool> |
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| diff -r e1502e4f8725 -r 57db282ca204 data_manager/test.json --- a/data_manager/test.json Wed Feb 21 19:26:53 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +0,0 @@ -{ - "data_tables": { - "omamer_data": [ - { - "name": "Primates-v2.0", - "path": "database_omamer", - "value": "Primates-v2.0", - "version": "2.0.2" - } - ] - } -} \ No newline at end of file |
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| diff -r e1502e4f8725 -r 57db282ca204 data_manager_conf.xml --- a/data_manager_conf.xml Wed Feb 21 19:26:53 2024 +0000 +++ b/data_manager_conf.xml Thu Mar 07 14:28:42 2024 +0000 |
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| @@ -6,8 +6,9 @@ <column name="value" /> <column name="name" /> <column name="version"/> - <column name="path" output_ref="out_file"> - <move type="directory" relativize_symlinks="True"> + <column name="path" output_ref="output_file"> + <move type="file"> + <source>${path}</source> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">omamer/${value}</target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/omamer/${value}</value_translation> @@ -16,4 +17,4 @@ </output> </data_table> </data_manager> -</data_managers> \ No newline at end of file +</data_managers> |
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| diff -r e1502e4f8725 -r 57db282ca204 test-data/omamer.loc --- a/test-data/omamer.loc Wed Feb 21 19:26:53 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -# this is a tab separated file describing the location of OMAmer databases used for the -# OMAmer annotation tool -# -# the columns are: -# value name version path -# -# for example -# Primates-v2.0.0 Primates 2.0.2 /tmp/database/omamer/database_omamer/Primates-v2.0.0 \ No newline at end of file |
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| diff -r e1502e4f8725 -r 57db282ca204 test-data/out.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.json Thu Mar 07 14:28:42 2024 +0000 |
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| @@ -0,0 +1,12 @@ +{ + "data_tables": { + "omamer": [ + { + "name": "Primates-v2.0.0", + "path": "Primates-v2.0.0.h5", + "value": "Primates-v2.0.0.h5", + "version": "2.0.2" + } + ] + } +} \ No newline at end of file |
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| diff -r e1502e4f8725 -r 57db282ca204 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Wed Feb 21 19:26:53 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<tables> - <table name="omamer" comment_char="#"> - <columns>value, name, version, path</columns> - <file path="${__HERE__}/test-data/omamer.loc"/> - </table> -</tables> \ No newline at end of file |