# HG changeset patch
# User thanhlv
# Date 1550507954 18000
# Node ID 87341275b335f2e5a370b65ea166ba65f6f2dd98
# Parent  8beb2af51dc5233b41f8df77fe6106122eda28cd
Deleted selected files

diff -r 8beb2af51dc5 -r 87341275b335 data_manager_build_ariba_database/data_manager/ariba_data_base_builder.py
--- 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
diff -r 8beb2af51dc5 -r 87341275b335 data_manager_build_ariba_database/data_manager/ariba_database_builder.xml
--- 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>
diff -r 8beb2af51dc5 -r 87341275b335 data_manager_build_ariba_database/data_manager/ariba_database_builder.xml.bk
--- 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>
diff -r 8beb2af51dc5 -r 87341275b335 data_manager_build_ariba_database/data_manager_conf.xml
--- 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>
diff -r 8beb2af51dc5 -r 87341275b335 data_manager_build_ariba_database/macros.xml
--- 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
diff -r 8beb2af51dc5 -r 87341275b335 data_manager_build_ariba_database/tool-data/ariba_databases.loc.sample
diff -r 8beb2af51dc5 -r 87341275b335 data_manager_build_ariba_database/tool_data_table_conf.xml.sample
--- 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>
diff -r 8beb2af51dc5 -r 87341275b335 help-command.txt
--- 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
diff -r 8beb2af51dc5 -r 87341275b335 planemo_command/planemo_command_ariba.sh
--- 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
diff -r 8beb2af51dc5 -r 87341275b335 planemo_command/planemo_command_ariba_flag.sh
--- 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
diff -r 8beb2af51dc5 -r 87341275b335 test.ipynb
--- 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
-}