changeset 4:55d34d89fb76 draft

Deleted selected files

--- a/help-command.txt	Mon Feb 18 11:48:39 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 11:48:39 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 11:48:39 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 11:48:39 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
-}