changeset 2:c9896bb1f03c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f

--- a/data_manager/twobit_builder.py	Thu Jan 19 11:45:29 2017 -0500
+++ b/data_manager/twobit_builder.py	Tue Apr 04 17:54:54 2017 -0400
@@ -1,19 +1,23 @@
 #!/usr/bin/env python
-#Dan Blankenberg
+# Dan Blankenberg
+from __future__ import print_function
 
-import sys, os, tempfile, optparse, uuid, subprocess
+import optparse
+import os
+import subprocess
+import sys
+import tempfile
+from json import dumps, loads
 
-from json import loads, dumps
+CHUNK_SIZE = 2**20  # 1mb
 
 
-CHUNK_SIZE = 2**20 #1mb
-
 def get_id_name( params, dbkey, fasta_description=None):
-    #TODO: ensure sequence_id is unique and does not already appear in location file
+    # TODO: ensure sequence_id is unique and does not already appear in location file
     sequence_id = params['param_dict']['sequence_id']
     if not sequence_id:
-        sequence_id = dbkey #uuid.uuid4() generate and use an uuid
-    
+        sequence_id = dbkey  # uuid.uuid4() generate and use an uuid
+
     sequence_name = params['param_dict']['sequence_name']
     if not sequence_name:
         sequence_name = fasta_description
@@ -21,18 +25,19 @@
             sequence_name = dbkey
     return sequence_id, sequence_name
 
+
 def build_twobit( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name ):
     twobit_base_name = "%s.2bit" % ( sequence_id )
     twobit_filename = os.path.join( target_directory, twobit_base_name )
-    
+
     args = [ 'faToTwoBit', fasta_filename, twobit_filename ]
-    tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-twobit-builder-stderr" )
+    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()
     if return_code:
         tmp_stderr.flush()
         tmp_stderr.seek(0)
-        print >> sys.stderr, "Error building index:"
+        print("Error building index:", file=sys.stderr)
         while True:
             chunk = tmp_stderr.read( CHUNK_SIZE )
             if not chunk:
@@ -40,53 +45,55 @@
             sys.stderr.write( chunk )
         sys.exit( return_code )
     tmp_stderr.close()
-    #lastz_seqs
+    # lastz_seqs
     data_table_entry = dict( value=sequence_id, name=sequence_name, path=twobit_base_name )
 
     _add_data_table_entry( data_manager_dict, "lastz_seqs", data_table_entry )
-    #twobit.loc
+    # twobit.loc
     data_table_entry = dict( value=sequence_id, path=twobit_base_name )
 
     _add_data_table_entry( data_manager_dict, "twobit", data_table_entry )
-    #alignseq
+    # alignseq
     data_table_entry = dict( type="seq", value=sequence_id, path=twobit_base_name )
 
     _add_data_table_entry( data_manager_dict, "alignseq_seq", data_table_entry )
 
+
 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
     data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
     data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
     data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
     return data_manager_dict
 
+
 def main():
-    #Parse Command Line
     parser = optparse.OptionParser()
     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' )
     (options, args) = parser.parse_args()
-    
+
     filename = args[0]
-    
+
     params = loads( open( filename ).read() )
 
     target_directory = params[ 'output_data' ][0]['extra_files_path']
     os.mkdir( target_directory )
     data_manager_dict = {}
-    
+
     dbkey = options.fasta_dbkey
-    
+
     if dbkey in [ None, '', '?' ]:
         raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
-    
+
     sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
-    
-    #build the index
+
+    # build the index
     build_twobit( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name )
-    
-    #save info to json file
+
+    # save info to json file
     open( filename, 'wb' ).write( dumps( data_manager_dict ) )
-        
-if __name__ == "__main__": main()
+
 
+if __name__ == "__main__":
+    main()

--- a/data_manager/twobit_builder.xml	Thu Jan 19 11:45:29 2017 -0500
+++ b/data_manager/twobit_builder.xml	Tue Apr 04 17:54:54 2017 -0400
@@ -3,14 +3,19 @@
         <requirement type="package" version="324">ucsc-fatotwobit</requirement>
     </requirements>
     <description>builder</description>
-    <command interpreter="python">twobit_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}"</command>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/twobit_builder.py'
+        '${out_file}'
+        --fasta_filename '${all_fasta_source.fields.path}'
+        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
+        --fasta_description '${all_fasta_source.fields.name}'
+    ]]></command>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta"/>
         </param>
-        <param type="text" name="sequence_name" value="" label="Name of sequence" />
-        <param type="text" name="sequence_id" value="" label="ID for sequence" />
-        
+        <param name="sequence_name" type="text" value="" label="Name of sequence" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>
@@ -25,11 +30,9 @@
     </tests>
 
     <help>
-
 .. class:: infomark
 
-**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
-
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
     </help>
 </tool>