--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Mon Apr 10 09:37:45 2017 -0400
@@ -0,0 +1,13 @@
+name: plant_tribes_gene_family_aligner
+owner: greg
+description: |
+  Contains a tool that integrates de novo assembly sequences with scaffold gene family sequences.
+homepage_url: https://github.com/dePamphilis/PlantTribes
+long_description: |
+  Contains a tool that tool is one of the PlantTribes collection of automated modular analysis pipelines that
+  utilize objective classifications of complete protein sequences from sequenced plant genomes to perform
+  comparative evolutionary studies.  This tool aligns gene family sequences.
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/plant_tribes/gene_family_aligner
+type: unrestricted
+categories:
+- Phylogenetics

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_family_aligner.py	Mon Apr 10 09:37:45 2017 -0400
@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+import argparse
+import os
+import subprocess
+
+import utils
+
+OUTPUT_DIR = 'geneFamilyAlignments_dir'
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--alignment_method', dest='alignment_method', help='Multiple sequence alignments method')
+parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help="Trims alignments using trimAl's ML heuristic trimming approach")
+parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help="Flag for constructing orthogroup multiple codon alignments")
+parser.add_argument('--gap_trimming', dest='gap_trimming', default=None, type=float, help='Remove sites in alignments with gaps of')
+parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=None, help='"Maximum number of iterations')
+parser.add_argument('--method', dest='method', help='Protein clustering method')
+parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
+parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets")
+parser.add_argument('--output', dest='output', help="Output dataset")
+parser.add_argument('--output_dir', dest='output_dir', help="Output dataset file_path directory")
+parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='"Maximum number of iteration that the PASTA algorithm will execute')
+parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta')
+parser.add_argument('--remove_sequences', dest='remove_sequences', default=None, type=float, help='Remove sequences with gaps of')
+parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
+
+args = parser.parse_args()
+
+# Build the command line.
+cmd = 'GeneFamilyAligner'
+cmd += ' --orthogroup_faa %s' % args.orthogroup_faa
+cmd += ' --scaffold %s' % args.scaffold
+cmd += ' --method %s' % args.method
+cmd += ' --alignment_method %s' % args.alignment_method
+if args.alignment_method == 'pasta':
+    if args.pasta_script_path is not None:
+        cmd += ' --pasta_script_path %s' % args.pasta_script_path
+    if args.pasta_iter_limit is not None:
+        cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit
+cmd += ' --num_threads %d' % args.num_threads
+if args.codon_alignments is not None:
+    cmd += ' --codon_alignments'
+if args.automated_trimming is not None:
+    cmd += ' --automated_trimming'
+if args.gap_trimming is not None:
+    cmd += ' --gap_trimming %4f' % args.gap_trimming
+if args.remove_sequences is not None:
+    cmd += ' --remove_sequences %4f' % args.remove_sequences
+if args.iterative_realignment is not None:
+    cmd += ' --iterative_realignment %d' % args.iterative_realignment
+# 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)
+if args.codon_alignments is None:
+    src_output_dir = OUTPUT_DIR
+else:
+    src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln')
+utils.move_directory_files(src_output_dir, args.output_dir)
+utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plant_tribes_scaffolds.loc.sample	Mon Apr 10 09:37:45 2017 -0400
@@ -0,0 +1,4 @@
+## Plant Tribes scaffolds
+#Value	Name	Path	Description
+#22Gv1.0	22Gv1.0	/plant_tribes/scaffolds/22Gv1.0	22 plant genomes (Angiosperms clusters, version 1.0; 22Gv1.0)
+#22Gv1.1	22Gv1.1	/plant_tribes/scaffolds/22Gv1.1	22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_pasta.py	Mon Apr 10 09:37:45 2017 -0400
@@ -0,0 +1,63 @@
+#! /usr/bin/env python
+
+"""Main script of PASTA in command-line mode - this simply invokes the main
+    function found in pasta/mainpasta.py
+"""
+
+# This file is part of PASTA which is forked from SATe
+
+# PASTA like SATe is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# Jiaye Yu and Mark Holder, University of Kansas
+
+if __name__ == "__main__":
+    import os
+    import sys
+    from pasta.mainpasta import pasta_main
+    from pasta import MESSENGER
+    sys.setrecursionlimit(100000)
+    _PASTA_DEBUG = os.environ.get('PASTA_DEBUG')
+    _DEVELOPER = _PASTA_DEBUG and _PASTA_DEBUG != '0'
+
+    if not _DEVELOPER:
+        _PASTA_DEVELOPER = os.environ.get('PASTA_DEVELOPER')
+        _DEVELOPER = _PASTA_DEVELOPER and _PASTA_DEVELOPER != '0'
+    try:
+        rc, temp_dir, temp_fs = pasta_main()
+        if not rc:
+            raise ValueError("Unknown PASTA execution error")
+        if (temp_dir is not None) and (os.path.exists(temp_dir)):
+            MESSENGER.send_info("Note that temporary files from the run have not been deleted, they can be found in:\n   '%s'\n" % temp_dir)
+            if sys.platform.lower().startswith('darwin') and ("'" not in temp_dir):
+                MESSENGER.send_info('''
+If you cannot see this directory in the Finder application, you may want to use
+the 'open' command executed from a Terminal.  You can do this by launching the
+/Applications/Utilities/Terminal program and then typing
+
+open '%s'
+
+followed by a return at the prompt. If the argument to the open command is a
+directory, then it should open a Finder window in the directory (even if that
+directory is hidden by default).
+''' % temp_dir)
+    except Exception, x:
+        if _DEVELOPER:
+            raise
+        message = "PASTA is exiting because of an error:\n%s " % str(x)
+        try:
+            from pasta import MESSENGER
+            MESSENGER.send_error(message)
+        except:
+            sys.stderr.write(message)
+        sys.exit(1)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Apr 10 09:37:45 2017 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="plant_tribes_scaffolds" comment_char="#">
+        <columns>value, name, path, description</columns>
+        <file path="tool-data/plant_tribes_scaffolds.loc" />
+    </table>
+</tables>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.py	Mon Apr 10 09:37:45 2017 -0400
@@ -0,0 +1,42 @@
+import os
+import shutil
+import sys
+
+
+def check_execution_errors(rc, stderr):
+    if rc != 0:
+        stop_err(stderr.read())
+
+
+def move_directory_files(source_dir, destination_dir):
+    source_directory = os.path.abspath(source_dir)
+    destination_directory = os.path.abspath(destination_dir)
+    if not os.path.isdir(destination_directory):
+        os.makedirs(destination_directory)
+    for dir_entry in os.listdir(source_directory):
+        source_entry = os.path.join(source_directory, dir_entry)
+        shutil.move(source_entry, destination_directory)
+
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit(1)
+
+
+def write_html_output(output, title, dir):
+    with open(output, 'w') as fh:
+        fh.write('<html><head><h3>%s</h3></head>\n' % title)
+        fh.write('<body><p/><table cellpadding="2">\n')
+        fh.write('<tr><th>Size</th><th>Name</th></tr>\n')
+        for index, fname in enumerate(sorted(os.listdir(dir))):
+            if index % 2 == 0:
+                bgcolor = '#D8D8D8'
+            else:
+                bgcolor = '#FFFFFF'
+            try:
+                size = str(os.path.getsize(os.path.join(dir, fname)))
+            except:
+                size = 'unknown'
+            link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname)
+            fh.write('<tr bgcolor="%s"><td>%s</td><td>%s</td></tr>\n' % (bgcolor, size, link))
+        fh.write('</table></body></html>\n')