# HG changeset patch
# User greg
# Date 1504113108 14400
# Node ID 34ca28db0a5d55515012958fc31c7f78c1603d44
# Parent  1134528b93cc52b61088c1c94d4c6d47acbed751
Uploaded

diff -r 1134528b93cc -r 34ca28db0a5d .shed.yml
--- a/.shed.yml	Fri Aug 25 13:01:04 2017 -0400
+++ b/.shed.yml	Wed Aug 30 13:11:48 2017 -0400
@@ -8,7 +8,7 @@
   complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
   analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
   GeneFamilyAligner tool.
-remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/plant_tribes/gene_family_phylogeny_builder
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_phylogeny_builder
 type: unrestricted
 categories:
 - Phylogenetics
diff -r 1134528b93cc -r 34ca28db0a5d gene_family_phylogeny_builder.py
--- a/gene_family_phylogeny_builder.py	Fri Aug 25 13:01:04 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)
diff -r 1134528b93cc -r 34ca28db0a5d gene_family_phylogeny_builder.xml
--- a/gene_family_phylogeny_builder.xml	Fri Aug 25 13:01:04 2017 -0400
+++ b/gene_family_phylogeny_builder.xml	Wed Aug 30 13:11:48 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.2">
+<tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.2.1">
     <description>builds phylogenetic trees of aligned orthologous gene family clusters</description>
     <macros>
         <import>macros.xml</import>
@@ -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.