Mercurial > repos > thanhlv > ariba
changeset 2:87341275b335 draft
Deleted selected files
author | thanhlv |
---|---|
date | Mon, 18 Feb 2019 11:39:14 -0500 |
parents | 8beb2af51dc5 |
children | 6aabe4f367fd |
files | data_manager_build_ariba_database/data_manager/ariba_data_base_builder.py data_manager_build_ariba_database/data_manager/ariba_database_builder.xml data_manager_build_ariba_database/data_manager/ariba_database_builder.xml.bk data_manager_build_ariba_database/data_manager_conf.xml data_manager_build_ariba_database/macros.xml data_manager_build_ariba_database/tool-data/ariba_databases.loc.sample data_manager_build_ariba_database/tool_data_table_conf.xml.sample help-command.txt planemo_command/planemo_command_ariba.sh planemo_command/planemo_command_ariba_flag.sh test.ipynb |
diffstat | 10 files changed, 0 insertions(+), 383 deletions(-) [+] |
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--- a/data_manager_build_ariba_database/data_manager/ariba_data_base_builder.py Mon Feb 18 11:36:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ -import argparse -import json -import os -import shutil - - -def main(args): - output_path = os.getcwd() - db_folder = [d for d in os.listdir(output_path) if os.path.isdir(d)] - params = json.loads(open(args.output).read()) - target_directory = params['output_data'][0]['extra_files_path'] - os.mkdir(target_directory) - data_manager_entry = [] - for db in db_folder: - print("Current: ".format(os.path.join(output_path, d))) - print("Target: {}".format(target_directory)) - shutil.move(os.path.join(output_path, d), os.path.join(target_directory, d)) - data_manager_entry.append(dict(value=db.lower(), - name=db, - path=target_directory) - ) - data_manager_json = dict(data_tables=dict(ariba_databases=data_manager_entry)) - file(args.output, 'w').write(json.dumps(data_manager_json)) - - -if __name__ == '__main__': - parser = argparse.ArgumentParser(description='Create data manager json.') - # parser.add_argument('--db', dest='database', action='store', help='Database name') - parser.add_argument('--out', dest='output', action='store', help='JSON filename') - args = parser.parse_args() - main(args) - \ No newline at end of file
--- a/data_manager_build_ariba_database/data_manager/ariba_database_builder.xml Mon Feb 18 11:36:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,59 +0,0 @@ -<?xml version="1.0"?> -<tool id="ariba_database_builder" name="ARIBA build database" tool_type="manage_data" version="@VERSION@"> - <description>database builder</description> - <expand macro="requirements" /> - <version_command>ariba version | head head -n 1</version_command> - <command detect_errors="exit_code"> - <![CDATA[ - #if str($library.lib_type) == "curated" - #set $library_list = str($library.curated).split(',') - #for $library_ in $library_list: - #if str($library_) != 'None': - ariba getref '$library_' _tmp_db && ariba prepareref -f _tmp_db.fa -m _tmp_db.tsv '$library_' && - #end if - #end for - #end if - - #if str($library.lib_type) == "fasta" - #if str($library).fasta != 'None': - ariba prepareref --all_coding '$coding' -f '$library.fasta' '$library.db_name' - #end if - #end if - - python '$__tool_directory__/ariba_data_base_builder.py' --out '${out_file}' - ]]> - </command> - <inputs> - <conditional name="library"> - <param name="lib_type" type="select" label="Input reads type or collection" help="Select a curated database or a fasta from the history"> - <option value="curated" selected="true">Curated Database</option> - <option value="fasta">A fasta file</option> - </param> - <when value="curated"> - <param name="curated" type="select" multiple="true" label="Select partial library to download"> - <option value="card">CARD</option> - <option value="resfinder">Resfinder</option> - <option value="plasmidfinder">Plasmidfinder</option> - <option value="megares">Megares</option> - <option value="argannot">Argannot</option> - <option value="vfdb_core">vfdb_core</option> - <option value="vfdb_full">vfdb_full</option> - <option value="virulencefinder">virulencefinder</option> - </param> - </when> - <when value="fasta"> - <param name="fasta" type="data" format="fasta" optional="false" /> - <param name="db_name" type="text" label="DB name" help = "The DB name should include no space and special characters" /> - <param name="coding" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="Coding sequence?" /> - </when> - </conditional> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json" /> - </outputs> - <help> - </help> - <citations> - <citation type="doi">110.1099/mgen.0.000131</citation> - </citations> -</tool>
--- a/data_manager_build_ariba_database/data_manager/ariba_database_builder.xml.bk Mon Feb 18 11:36:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -<?xml version="1.0"?> -<tool id="ariba_database_builder" name="ARIBA build database" tool_type="manage_data" version="@VERSION@"> - <description>database builder</description> - <expand macro="requirements" /> - <version_command>ariba version | head head -n 1</version_command> - <command detect_errors="exit_code"> - <![CDATA[ - #set $library_list = str($libraries).split(',') - mkdir ariba-database && cd ariba-database && - #for $library in $library_list: - #if str($library) != 'None': - ariba getref $library _tmp_db && ariba prepareref -f _tmp_db.fa -m _tmp_db.tsv $library && - #end if - #end for - #for $fasta in $input_fasta: - #if str($fasta) != 'None': - ariba preparef --all_coding no $fasta $fasta && - #end if - #end for - cd .. && - python '$__tool_directory__/ariba_data_base_builder.py' --db '${database_name}' --out '${out_file}' - ]]> - </command> - <inputs> - <param name="database_name" type="text" label="Name for this database" /> - <param name="libraries" type="select" multiple="true" label="Select partial library to download"> - <option value="card">CARD</option> - <option value="resfinder">Resfinder</option> - <option value="plasmidfinder">Plasmidfinder</option> - </param> - <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" /> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json" /> - </outputs> - <help> - </help> - <citations> - <citation type="doi">110.1099/mgen.0.000131</citation> - </citations> -</tool>
--- a/data_manager_build_ariba_database/data_manager_conf.xml Mon Feb 18 11:36:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -<?xml version="1.0"?> -<data_managers> - <data_manager tool_file="data_manager/ariba_database_builder.xml" id="ariba_database_builder" version="2.12.2"> - <data_table name="ariba_databases"> - <output> - <column name="value" /> - <column name="name" /> - <column name="path" output_ref="out_file"> - <move type="directory" relativize_symlinks="True"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">ariba_databases/${value}</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/ariba_databases/${value}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - </output> - </data_table> - </data_manager> -</data_managers>
--- a/data_manager_build_ariba_database/macros.xml Mon Feb 18 11:36:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -<macros> - <token name="@VERSION@">0.1.0</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="2.13.2">ariba</requirement> - </requirements> - </xml> - - <xml name="version_command"> - <version_command>ariba version | head -n 1</version_command> - </xml> - - <xml name="citations"> - <citations> - <citation type="doi">10.1099/mgen.0.000131</citation> - </citations> - </xml> - -</macros> \ No newline at end of file
--- a/data_manager_build_ariba_database/tool_data_table_conf.xml.sample Mon Feb 18 11:36:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -<?xml version="1.0"?> -<tables> - <!-- Locations of ARIBA database in the required format --> - <table name="ariba_databases" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/ariba_databases.loc" /> - </table> -</tables>
--- a/help-command.txt Mon Feb 18 11:36:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -usage: ariba <command> <options> - -ARIBA: Antibiotic Resistance Identification By Assembly - -optional arguments: - -h, --help show this help message and exit - -Available commands: - - aln2meta Converts multi-aln fasta and SNPs to metadata - expandflag Expands flag column of report file - flag Translate the meaning of a flag - getref Download reference data - micplot Make violin/dot plots using MIC data - prepareref Prepare reference data for input to "run" - pubmlstget Download species from PubMLST and make db - pubmlstspecies - Get list of available species from PubMLST - refquery Get cluster or sequence info from prepareref output - run Run the local assembly pipeline - summary Summarise multiple reports made by "run" - test Run small built-in test dataset - version Get versions and exit
--- a/planemo_command/planemo_command_ariba.sh Mon Feb 18 11:36:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -#!/usr/bin/env bash -planemo tool_init \ - --force \ - --id "ariba_run" \ - --name "Antimicrobial Resistance Identification By Assembly" \ - --requirement ariba@2.13.1 \ - --example_command 'ariba run $DBNAME reads1.fastq reads2.fastq out.run' \ - --example_input 2.fastq \ - --example_output out.run \ - --cite_url 'https://github.com/sanger-pathogens/ariba' \ No newline at end of file
--- a/planemo_command/planemo_command_ariba_flag.sh Mon Feb 18 11:36:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -#!/usr/bin/env bash -planemo tool_init \ - --force \ - --id "ariba_flag" \ - --name "Antimicrobial Resistance Identification By Assembly" \ - --requirement ariba@2.13.1 \ - --example_command 'ariba run $DBNAME reads1.fastq reads2.fastq out.run' \ - --example_input 2.fastq \ - --example_output out.run \ - --cite_url 'https://github.com/sanger-pathogens/ariba' \ No newline at end of file
--- a/test.ipynb Mon Feb 18 11:36:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,163 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "name = \"thanh\"\n", - "data_manager_entry = {}\n", - "data_manager_entry['value'] = name.lower()\n", - "data_manager_entry['name'] = name\n", - "data_manager_entry['path'] = '.'\n", - "data_manager_json = dict(data_tables=dict(busco=data_manager_entry))" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'value': 'thanh', 'name': 'thanh', 'path': '.'}" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "data_manager_entry" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'data_tables': {'busco': {'value': 'thanh', 'name': 'thanh', 'path': '.'}}}" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "data_manager_json" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [], - "source": [ - "import os\n", - "directories=[d for d in os.listdir(os.getcwd()) if os.path.isdir(d)]" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[{'value': 'database', 'name': 'DATABASE'},\n", - " {'value': 'data_manager_build_ariba_database',\n", - " 'name': 'DATA_MANAGER_BUILD_ARIBA_DATABASE'},\n", - " {'value': 'test-data', 'name': 'TEST-DATA'},\n", - " {'value': 'tool-data', 'name': 'TOOL-DATA'},\n", - " {'value': 'planemo_command', 'name': 'PLANEMO_COMMAND'},\n", - " {'value': '.ipynb_checkpoints', 'name': '.IPYNB_CHECKPOINTS'},\n", - " {'value': '.git', 'name': '.GIT'}]" - ] - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "a_db = []\n", - "for d in directories:\n", - " dict_entry = dict(value=d,name=d.upper())\n", - " a_db.append(dict_entry)\n", - "a_db" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [], - "source": [ - "data_manager_json = dict(ariba_databases=a_db)" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'ariba_databases': [{'value': 'database', 'name': 'DATABASE'},\n", - " {'value': 'data_manager_build_ariba_database',\n", - " 'name': 'DATA_MANAGER_BUILD_ARIBA_DATABASE'},\n", - " {'value': 'test-data', 'name': 'TEST-DATA'},\n", - " {'value': 'tool-data', 'name': 'TOOL-DATA'},\n", - " {'value': 'planemo_command', 'name': 'PLANEMO_COMMAND'},\n", - " {'value': '.ipynb_checkpoints', 'name': '.IPYNB_CHECKPOINTS'},\n", - " {'value': '.git', 'name': '.GIT'}]}" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "data_manager_json" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 2", - "language": "python", - "name": "python2" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.6.6" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -}