--- a/gene_family_phylogeny_builder.py	Fri Aug 25 13:00:37 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import os
-
-import utils
-
-OUTPUT_DIR = 'geneFamilyPhylogenies_dir'
-
-parser = argparse.ArgumentParser()
-
-parser.add_argument('--alignment_type', dest='alignment_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_phylip', dest='output_phylip', default=None, help='Output for orthogroup phylip multiple sequence alignments')
-parser.add_argument('--output_phylip_dir', dest='output_phylip_dir', default=None, help='output_phylip.files_path')
-parser.add_argument('--output_tree', dest='output_tree', default=None, help='Output for phylogenetic trees')
-parser.add_argument('--output_tree_dir', dest='output_tree_dir', default=None, help='output_tree.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.alignment_type
-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.
-utils.run_command(cmd)
-
-# Handle outputs.
-if args.output_phylip is not None and args.output_phylip_dir is not None:
-    src_output_dir = os.path.join(OUTPUT_DIR, 'phylip_aln')
-    utils.move_directory_files(src_output_dir, args.output_phylip_dir)
-    utils.write_html_output(args.output_phylip, 'Orthogroup phylip multiple sequence alignments', args.output_phylip_dir)
-if args.output_tree is not None and args.output_tree_dir is not None:
-    src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree')
-    utils.move_directory_files(src_output_dir, args.output_tree_dir, copy=True)
-    utils.write_html_output(args.output_tree, 'Phylogenetic trees', args.output_tree_dir)

--- a/gene_family_phylogeny_builder.xml	Fri Aug 25 13:00:37 2017 -0400
+++ b/gene_family_phylogeny_builder.xml	Fri Aug 25 13:23:01 2017 -0400
@@ -16,7 +16,7 @@
     #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
 #end if
 
-python '$__tool_directory__/gene_family_phylogeny_builder.py'
+GeneFamilyPhylogenyBuilder
 #if str($input_format) == 'ptalign':
     --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path'
     --alignment_type aln
@@ -53,16 +53,10 @@
         ## configuration will be used if the --rooting_order flag is missing.
     #end if
     --bootstrap_replicates $bootstrap_replicates
-    --output_phylip '$output_phylip'
-    --output_phylip_dir '$output_phylip.files_path'
 #end if
 --min_orthogroup_size $min_orthogroup_size
 --max_orthogroup_size $max_orthogroup_size
 --num_threads \${GALAXY_SLOTS:-4}
-#if str($output_pttree_dir) == 'yes':
-    --output_tree '$output_tree'
-    --output_tree_dir '$output_tree.files_path'
-#end if
     ]]></command>
     <inputs>
         <conditional name="input_format_cond">
@@ -132,21 +126,15 @@
         </conditional>
         <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" />
         <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" />
-        <param name="output_pttree_dir" type="select" label="Output additional directory of phylogenetic tree files?">
-            <option value="no" selected="true">No</option>
-            <option value="yes">Yes</option>
-        </param>
     </inputs>
     <outputs>
-        <collection name="tree" type="list" label="${tool.name} (phylogenetic trees, dataset collection) on ${on_string}">
+        <collection name="tree" type="list" label="${tool.name} (phylogenetic trees) on ${on_string}">
             <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
         </collection>
-        <data name="output_tree" format="pttree" label="${tool.name} (phylogenetic trees, directory) on ${on_string}">
-            <filter>output_pttree_dir == 'yes'</filter>
-        </data>
-        <data name="output_phylip" format="ptphylip" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}">
+        <collection name="phylip" type="list" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}">
             <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
-        </data>
+            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" />
+        </collection>
     </outputs>
     <tests>
         <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.