--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_family_phylogeny_builder.py	Tue Apr 11 11:05:24 2017 -0400
@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+import argparse
+import subprocess
+
+import utils
+
+OUTPUT_DIR = 'phylogenomicsAnalysis_dir'
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--alignments_type', dest='alignments_type', help='Input alignments type produced by the GeneFamilyAligner')
+parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis')
+parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files')
+parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, help='Maximum number of sequences in orthogroup alignments')
+parser.add_argument('--method', dest='method', help='Protein clustering method')
+parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, help='Minimum number of sequences in orthogroup alignments')
+parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
+parser.add_argument('--orthogroup_aln', dest='orthogroup_aln', help="Input dataset files_path")
+parser.add_argument('--output', dest='output', help='Output for phylogenetic trees')
+parser.add_argument('--output_dir', dest='output_dir', help='output.files_path')
+parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees')
+parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
+parser.add_argument('--sequence_type', dest='sequence_type', help="Sequence type used in the phylogenetic inference")
+parser.add_argument('--tree_inference', dest='tree_inference', help='Phylogenetic trees inference method')
+
+args = parser.parse_args()
+
+# Build the command line.
+cmd = 'GeneFamilyPhylogenyBuilder'
+cmd += ' --alignment_type %s' % args.tree_inference
+if args.bootstrap_replicates is not None:
+    cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates
+cmd += ' --config_dir %s' % args.config_dir
+cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size
+cmd += ' --method %s' % args.method
+cmd += ' --min_orthogroup_size %d' % args.min_orthogroup_size
+cmd += ' --num_threads %d' % args.num_threads
+cmd += ' --orthogroup_aln %s' % args.orthogroup_aln
+if args.rooting_order is not None:
+    cmd += ' --rooting_order %s' % args.rooting_order
+cmd += ' --scaffold %s' % args.scaffold
+cmd += ' --sequence_type %s' % args.sequence_type
+cmd += ' --tree_inference %s' % args.tree_inference
+# Run the command.
+proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
+rc = proc.wait()
+utils.check_execution_errors(rc, proc.stderr)
+utils.move_directory_files(OUTPUT_DIR, args.output_dir)
+utils.write_html_output(args.output, 'Phylogenetic trees', args.output_dir)