Mercurial > repos > thanhlv > ariba
changeset 3:6aabe4f367fd draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ariba commit 067b5a6a02d5f04c2155b45eed5df257a1360645-dirty
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--- a/ariba_summary.xml Mon Feb 18 11:39:14 2019 -0500 +++ b/ariba_summary.xml Mon Feb 18 11:48:39 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="ariba_run" name="ARIBA summary" version="@VERSION@"> +<tool id="ariba_sum" name="ARIBA summary" version="@VERSION@"> <description> Summarises the results from one or more runs of ARIBA </description>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_build_ariba_database/data_manager/ariba_data_base_builder.py Mon Feb 18 11:48:39 2019 -0500 @@ -0,0 +1,32 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_build_ariba_database/data_manager/ariba_database_builder.xml Mon Feb 18 11:48:39 2019 -0500 @@ -0,0 +1,59 @@ +<?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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_build_ariba_database/data_manager/ariba_database_builder.xml.bk Mon Feb 18 11:48:39 2019 -0500 @@ -0,0 +1,41 @@ +<?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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_build_ariba_database/data_manager_conf.xml Mon Feb 18 11:48:39 2019 -0500 @@ -0,0 +1,18 @@ +<?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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_build_ariba_database/macros.xml Mon Feb 18 11:48:39 2019 -0500 @@ -0,0 +1,19 @@ +<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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_build_ariba_database/tool_data_table_conf.xml.sample Mon Feb 18 11:48:39 2019 -0500 @@ -0,0 +1,8 @@ +<?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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/help-command.txt Mon Feb 18 11:48:39 2019 -0500 @@ -0,0 +1,23 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_command/planemo_command_ariba.sh Mon Feb 18 11:48:39 2019 -0500 @@ -0,0 +1,10 @@ +#!/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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_command/planemo_command_ariba_flag.sh Mon Feb 18 11:48:39 2019 -0500 @@ -0,0 +1,10 @@ +#!/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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test.ipynb Mon Feb 18 11:48:39 2019 -0500 @@ -0,0 +1,163 @@ +{ + "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 +}