# HG changeset patch
# User iuc
# Date 1681632904 0
# Node ID 94bffa4fdedc6e85e8c5bfb6ca26823fdd8002d1
# Parent  b640d79b49cbcdbfa578b383a1c2483b4e2aaa79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 18d696a933873372ae5c77257fd31eaf2cd4ed13

diff -r b640d79b49cb -r 94bffa4fdedc data_manager/twobit_builder.py
--- a/data_manager/twobit_builder.py	Thu Nov 28 20:33:03 2019 +0000
+++ b/data_manager/twobit_builder.py	Sun Apr 16 08:15:04 2023 +0000
@@ -2,12 +2,12 @@
 # Dan Blankenberg
 from __future__ import print_function
 
+import json
 import optparse
 import os
 import subprocess
 import sys
 import tempfile
-from json import dumps, loads
 
 CHUNK_SIZE = 2**20  # 1mb
 
@@ -26,11 +26,14 @@
     return sequence_id, sequence_name
 
 
-def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name):
+def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, long):
     twobit_base_name = "%s.2bit" % (sequence_id)
     twobit_filename = os.path.join(target_directory, twobit_base_name)
 
-    args = ['faToTwoBit', fasta_filename, twobit_filename]
+    args = ['faToTwoBit']
+    if long:
+        args.append('-long')
+    args.extend([fasta_filename, twobit_filename])
     tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-twobit-builder-stderr")
     proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno())
     return_code = proc.wait()
@@ -42,7 +45,7 @@
             chunk = tmp_stderr.read(CHUNK_SIZE)
             if not chunk:
                 break
-            sys.stderr.write(chunk)
+            sys.stderr.write(chunk.decode('utf-8'))
         sys.exit(return_code)
     tmp_stderr.close()
     # lastz_seqs
@@ -71,11 +74,14 @@
     parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
     parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
     parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
+    parser.add_option('-l', '--long', dest='long', action="store_true", default=False, help='For big genomes you need to pass the -long option.')
+
     (options, args) = parser.parse_args()
 
     filename = args[0]
 
-    params = loads(open(filename).read())
+    with open(filename) as fh:
+        params = json.load(fh)
 
     target_directory = params['output_data'][0]['extra_files_path']
     os.mkdir(target_directory)
@@ -89,10 +95,11 @@
     sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
 
     # build the index
-    build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name)
+    build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.long)
 
     # save info to json file
-    open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True))
+    with open(filename, 'w') as fh:
+        json.dump(data_manager_dict, fh, sort_keys=True)
 
 
 if __name__ == "__main__":
diff -r b640d79b49cb -r 94bffa4fdedc data_manager/twobit_builder.xml
--- a/data_manager/twobit_builder.xml	Thu Nov 28 20:33:03 2019 +0000
+++ b/data_manager/twobit_builder.xml	Sun Apr 16 08:15:04 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="twobit_builder_data_manager" name="TwoBit" tool_type="manage_data" version="0.0.4" profile="19.05">
+<tool id="twobit_builder_data_manager" name="TwoBit" tool_type="manage_data" version="0.0.5" profile="19.05">
     <requirements>
         <requirement type="package" version="377">ucsc-fatotwobit</requirement>
         <requirement type="package" version="3.7">python</requirement>
@@ -7,6 +7,7 @@
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/twobit_builder.py'
 '${out_file}'
+$long
 --fasta_filename '${all_fasta_source.fields.path}'
 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
 --fasta_description '${all_fasta_source.fields.name}'
@@ -17,6 +18,7 @@
         </param>
         <param name="sequence_name" type="text" value="" label="Name of sequence" />
         <param name="sequence_id" type="text" value="" label="ID for sequence" />
+        <param argument="--long" type="boolean" truevalue="--long" falsevalue="" label="Use the -long option for very big genomes." />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>
diff -r b640d79b49cb -r 94bffa4fdedc data_manager_conf.xml
--- a/data_manager_conf.xml	Thu Nov 28 20:33:03 2019 +0000
+++ b/data_manager_conf.xml	Sun Apr 16 08:15:04 2023 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <data_managers>
     
-    <data_manager tool_file="data_manager/twobit_builder.xml" id="twobit_builder" version="0.0.2">
+    <data_manager tool_file="data_manager/twobit_builder.xml" id="twobit_builder">
         <data_table name="lastz_seqs">
             <output>
                 <column name="value" />