# HG changeset patch
# User dfornika
# Date 1522349723 14400
# Node ID b3856a35b527a33cbed885115d891c0030ce9e50
# Parent  8be8c9f08008bad2d620038c68b72d3be981dfcf
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/mentalist_v0.2 commit bbb2381b06b1509b5645bb09bc027f27ad6a99a2-dirty

diff -r 8be8c9f08008 -r b3856a35b527 data_managers/data_manager_conf.xml
--- a/data_managers/data_manager_conf.xml	Thu Mar 29 14:12:13 2018 -0400
+++ b/data_managers/data_manager_conf.xml	Thu Mar 29 14:55:23 2018 -0400
@@ -60,21 +60,4 @@
       </output>
     </data_table>
   </data_manager>
-  <!-- This Data Manager is a work-in-progress https://github.com/WGS-TB/MentaLiST/issues/33
-  <data_manager tool_file="data_manager_mentalist_remove_db/data_manager/mentalist_remove_db.xml" id="mentalist_remove_db" version="0.2.2">
-    <data_table name="mentalist_databases">
-      <output>
-        <column name="value" />
-        <column name="name" />
-        <column name="path" output_ref="out_file">
-          <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target>
-          </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path}</value_translation>
-          <value_translation type="function">abspath</value_translation>
-        </column>
-      </output>
-    </data_table>
-    </data_manager>
-  -->
 </data_managers>
diff -r 8be8c9f08008 -r b3856a35b527 data_managers/data_manager_mentalist_remove_db/data_manager/mentalist_remove_db.py
--- a/data_managers/data_manager_mentalist_remove_db/data_manager/mentalist_remove_db.py	Thu Mar 29 14:12:13 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-
-import argparse
-import json
-import os
-import shutil
-
-
-def main(args):
-    data_manager_entry = {}
-    data_manager_entry['value'] = args.database.lower()
-    data_manager_entry['name'] = args.database
-    data_manager_entry['path'] = '.'
-    data_manager_json = dict(data_tables=dict(kraken_databases=data_manager_entry))
-    params = json.loads(open(args.output).read())
-    target_directory = params['output_data'][0]['extra_files_path']
-    os.mkdir(target_directory)
-    output_path = os.path.join(os.getcwd(), 'kraken-database')
-    for filename in os.listdir(output_path):
-        shutil.move(os.path.join(output_path, filename), target_directory)
-    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)
diff -r 8be8c9f08008 -r b3856a35b527 data_managers/data_manager_mentalist_remove_db/data_manager/mentalist_remove_db.xml
--- a/data_managers/data_manager_mentalist_remove_db/data_manager/mentalist_remove_db.xml	Thu Mar 29 14:12:13 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-<?xml version="1.0"?>
-<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.2.2">
-  <requirements>
-    <requirement type="package" version="0.2.2">mentalist</requirement>
-  </requirements>
-  <command detect_errors="exit_code">
-  <![CDATA[
-	   python '$__tool_directory__/mentalist_remove_db.py'
-	   --db '$database_name'
-  ]]>
-  </command>
-  <inputs>
-    <param name="kmer_db" type="select">
-      <options from_data_table="mentalist_databases">
-	<validator type="no_options" message="No MentaLiST databases are available" />
-      </options>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out_file" format="data_manager_json" />
-  </outputs>
-  <citations>
-    <citation type="doi">10.1101/172858</citation>
-    <citation type="doi">10.1099/mgen.0.000146</citation>
-  </citations>
-</tool>
diff -r 8be8c9f08008 -r b3856a35b527 data_managers/data_manager_mentalist_remove_db/tool-data/mentalist_databases.loc.sample
diff -r 8be8c9f08008 -r b3856a35b527 data_managers/data_manager_mentalist_remove_db/tool_data_table_conf.xml.sample
--- a/data_managers/data_manager_mentalist_remove_db/tool_data_table_conf.xml.sample	Thu Mar 29 14:12:13 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<?xml version="1.0"?>
-<tables>
-  <!--Locations of MentaLiST database in the required format -->
-  <table name="mentalist_databases" comment_char="#">
-    <columns>value, name, path</columns>
-      <file path="tool-data/mentalist_databases.loc" />
-  </table>
-</tables>
\ No newline at end of file