--- a/gene_family_aligner.xml	Fri Aug 25 13:00:09 2017 -0400
+++ b/gene_family_aligner.xml	Wed Sep 06 09:18:38 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.2">
+<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.3.0">
     <description>aligns integrated orthologous gene family clusters</description>
     <macros>
         <import>macros.xml</import>
@@ -8,15 +8,7 @@
 #set input_format = $input_format_cond.input_format
 #set alignment_method_cond = $input_format_cond.alignment_method_cond
 #set alignment_method = $alignment_method_cond.alignment_method
-#if str($input_format_cond.input_format) == 'ptortho':
-    #set output_codon_alignments = False
-#else if str($input_format_cond.input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments ) == 'no':
-    #set output_codon_alignments = False
-#else:
-    #set output_codon_alignments = True
-#end if
-
-python '$__tool_directory__/gene_family_aligner.py'
+GeneFamilyAligner
 --alignment_method $alignment_method
 #if str($alignment_method) == 'pasta':
     --pasta_script_path '$__tool_directory__/run_pasta.py'
@@ -29,7 +21,7 @@
     ## str($input_format) == 'ptorthocs'
     --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
     #if str($input_format_cond.codon_alignments) == 'yes':
-        --codon_alignments true
+        --codon_alignments
     #end if
 #end if
 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
@@ -40,7 +32,7 @@
         --gap_trimming $trim_type_cond.gap_trimming
     #else:
         ## str($trim_type) == 'automated_trimming'
-        --automated_trimming true
+        --automated_trimming
     #end if
     #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
     #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
@@ -51,33 +43,7 @@
         #if str($remove_sequences_with_gaps_cond.iterative_realignment):
             --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
         #end if
-        #if $output_codon_alignments:
-            --output '$output_aln_filtered_ca'
-            --output_dir '$output_aln_filtered_ca.files_path'
-        #else:
-            --output '$output_aln_filtered'
-            --output_dir '$output_aln_filtered.files_path'
-        #end if
-    #else:
-        #if $output_codon_alignments:
-            --output '$output_aln_trimmed_ca'
-            --output_dir '$output_aln_trimmed_ca.files_path'
-        #else:
-            --output '$output_aln_trimmed'
-            --output_dir '$output_aln_trimmed.files_path'
-        #end if
     #end if
-#else:
-    #if $output_codon_alignments:
-        --output '$output_aln_ca'
-        --output_dir '$output_aln_ca.files_path'
-    #else:
-        --output '$output_aln'
-        --output_dir '$output_aln.files_path'
-    #end if
-#end if
-#if str($output_dataset_collection) == 'yes':
-    --output_dataset_collection dataset_collection
 #end if
     ]]></command>
     <inputs>
@@ -107,27 +73,25 @@
         </param>
     </inputs>
     <outputs>
-        <data name="output_aln" format="ptalign" label="${tool.name} (proteins orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
-        </data>
-        <data name="output_aln_ca" format="ptalignca" label="${tool.name} (protein and coding sequences orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
-        </data>
-        <data name="output_aln_filtered" format="ptalignfiltered" label="${tool.name} (filtered proteins orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter>
-        </data>
-        <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="${tool.name} (filtered protein and coding sequences orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter>
-        </data>
-        <data name="output_aln_trimmed" format="ptaligntrimmed" label="${tool.name} (trimmed proteins orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
-        </data>
-        <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed protein and coding sequences orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
-        </data>
-        <collection name="dataset_collection" type="list" label="${tool.name} (dataset collection) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="dataset_collection" format="fasta" />
-            <filter>output_dataset_collection == 'yes'</filter>
+        <collection name="primary" type="list" label="${tool.name} (primary proteins orthogroup alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="orthogroups_aln" format="fasta" />
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
+        </collection>
+        <collection name="trimmed" type="list" label="${tool.name} (trimmed proteins orthogroup alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="orthogroups_aln" format="fasta" />
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
+        </collection>
+        <collection name="primary_trimmed" type="list" label="${tool.name} (primary proteins orthogroup alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="other_orthogroups_aln" format="fasta" />
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
+        </collection>
+        <collection name="filtered" type="list" label="${tool.name} (filtered proteins orthogroup alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="orthogroups_aln" format="fasta" />
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
+        </collection>
+        <collection name="primary_filtered" type="list" label="${tool.name} (primary and trimmed proteins orthogroup alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="other_orthogroups_aln" format="fasta" />
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
         </collection>
     </outputs>
     <tests>