# HG changeset patch
# User greg
# Date 1491831368 14400
# Node ID badd2d0f168955fed80614c63061cde059dceff3
# Parent  b52d29988df87a330532a622d0288f5cd94bbe8c
Uploaded

diff -r b52d29988df8 -r badd2d0f1689 .shed.yml
--- a/.shed.yml	Fri Apr 07 14:37:29 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-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
diff -r b52d29988df8 -r badd2d0f1689 gene_family_aligner.py
--- a/gene_family_aligner.py	Fri Apr 07 14:37:29 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-#!/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)
diff -r b52d29988df8 -r badd2d0f1689 gene_family_aligner.xml
--- a/gene_family_aligner.xml	Fri Apr 07 14:37:29 2017 -0400
+++ b/gene_family_aligner.xml	Mon Apr 10 09:36:08 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="0.8.0">
+<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.0">
     <description>aligns gene family sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -23,18 +23,11 @@
             --num_threads \${GALAXY_SLOTS:-4}
             #if str($input_format) == 'ptortho':
                 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
-                --output '$output_ptortho'
-                --output_dir '$output_ptortho.files_path'
             #else:
                 ## str($input_format) == 'ptorthocs'
                 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
                 #if str($input_format_cond.codon_alignments) == 'yes':
                     --codon_alignments 'true'
-                    --output '$output_ptorthocs'
-                    --output_dir '$output_ptorthocs.files_path'
-                #else:
-                    --output '$output_ptortho'
-                    --output_dir '$output_ptortho.files_path'
                 #end if
             #end if
             #if str($options_type_cond.options_type) == 'advanced':
@@ -57,6 +50,8 @@
                     #end if
                 #end if
             #end if
+            --output '$output'
+            --output_dir '$output.files_path'
         ]]>
     </command>
     <inputs>
@@ -88,12 +83,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output_ptortho" format="ptortho" label="Aligned gene family sequences on ${on_string}">
-            <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')</filter>
-        </data>
-        <data name="output_ptorthocs" format="ptorthocs" label="Aligned gene family sequences and corresponding coding sequences on ${on_string}">
-            <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes'</filter>
-        </data>
+        <data name="output" format="ptalign" label="Aligned gene family sequences on ${on_string}" />
     </outputs>
     <tests>
         <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
diff -r b52d29988df8 -r badd2d0f1689 macros.xml
--- a/macros.xml	Fri Apr 07 14:37:29 2017 -0400
+++ b/macros.xml	Mon Apr 10 09:36:08 2017 -0400
@@ -1,5 +1,6 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
+    <token name="@WRAPPER_VERSION@">0.8</token>
     <xml name="requirements_assembly_post_processor">
         <requirements>
             <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
@@ -25,6 +26,11 @@
             <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
         </requirements>
     </xml>
+    <xml name="requirements_gene_family_phylogeny_builder">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
+        </requirements>
+    </xml>
     <xml name="stdio">
         <stdio>
             <exit_code range="1:"/>
diff -r b52d29988df8 -r badd2d0f1689 plant_tribes_scaffolds.loc.sample
--- a/plant_tribes_scaffolds.loc.sample	Fri Apr 07 14:37:29 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-## 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)
diff -r b52d29988df8 -r badd2d0f1689 run_pasta.py
--- a/run_pasta.py	Fri Apr 07 14:37:29 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-#! /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)
diff -r b52d29988df8 -r badd2d0f1689 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Apr 07 14:37:29 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<tables>
-    <table name="plant_tribes_scaffolds" comment_char="#">
-        <columns>value, name, path, description</columns>
-        <file path="tool-data/plant_tribes_scaffolds.loc" />
-    </table>
-</tables>
diff -r b52d29988df8 -r badd2d0f1689 utils.py
--- a/utils.py	Fri Apr 07 14:37:29 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-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')