--- a/gene_family_classifier.xml	Thu Aug 24 13:26:35 2017 -0400
+++ b/gene_family_classifier.xml	Mon Oct 30 09:52:34 2017 -0400
@@ -1,9 +1,11 @@
-<tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="@WRAPPER_VERSION@.2">
+<tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="@WRAPPER_VERSION@.3.0">
     <description>classifies gene sequences into pre-computed orthologous gene family clusters</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements_gene_family_classifier" />
+    <requirements>
+        <requirement type="package" version="1.0.3">plant_tribes_gene_family_classifier</requirement>
+    </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #if str($options_type.options_type_selector) == 'advanced':
     #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
@@ -83,22 +85,7 @@
 
 #if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
     --save_hmmscan_log true
-    --hmmscan_log '$hmmscan_log'
-#end if
-#if $create_ortho_sequences:
-    #if $create_corresponding_coding_sequences:
-        --output_ptorthocs '$output_ptorthocs'
-        --output_ptorthocs_dir '$output_ptorthocs.files_path'
-    #else:
-        --output_ptortho '$output_ptortho'
-        --output_ptortho_dir '$output_ptortho.files_path'
-    #end if
-#end if
-#if $single_copy_orthogroup:
-    #if $create_ortho_sequences:
-        --output_ptsco '$output_ptsco'
-        --output_ptsco_dir '$output_ptsco.files_path'
-    #end if
+    --hmmscan_log '$output_hmmscan_log'
 #end if
     ]]></command>
     <inputs>
@@ -206,24 +193,19 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="hmmscan_log" format="txt" label="${tool.name} (hmmscan.log) on ${on_string}">
+        <data name="output_hmmscan_log" format="txt" label="${tool.name} (hmmscan.log) on ${on_string}">
             <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
         </data>
-        <data name="output_ptortho" format="ptortho" label="${tool.name} (gene family clusters) on ${on_string}">
-            <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'no'</filter>
-        </data>
-        <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (gene family clusters) on ${on_string}">
-            <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'yes'</filter>
-        </data>
-        <data name="output_ptsco" format="tabular" label="${tool.name} (single copy orthogroups) on ${on_string}">
+        <collection name="output_orthos" type="list" label="${tool.name} on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
+        </collection>
+        <collection name="output_orthogroups_fasta" type="list" label="${tool.name} (gene family clusters) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="output_orthogroups_fasta_dir" visible="false" ext="fasta" />
+            <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter>
+        </collection>
+        <collection name="output_single_copy_fasta" type="list" label="${tool.name} (single copy orthogroups) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="output_single_copy_fasta_dir" visible="false" ext="fasta" />
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
-            <change_format>
-                <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="no" format="ptortho" />
-                <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="yes" format="ptorthocs" />
-            </change_format>
-        </data>
-        <collection name="orthos" type="list">
-            <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
         </collection>
     </outputs>
     <tests>
@@ -235,8 +217,8 @@
             <param name="options_type_selector" value="advanced"/>
             <param name="create_orthogroup" value="yes"/>
             <param name="create_corresponding_coding_sequences" value="yes"/>
-            <output name="output_ptorthocs" file="output.ptorthocs" ftype="ptorthocs"/>
-            <output_collection name="orthos" type="list">
+            <param name="coding_sequences" value="transcripts.cleaned.nr.cds" ftype="fasta"/>
+            <output_collection name="output_orthos" type="list">
                 <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular" compare="contains"/>
                 <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
                 <element name="proteins.both.22Gv1.1.bestOrthos" file="proteins.both.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
@@ -244,6 +226,20 @@
                 <element name="proteins.hmmscan.22Gv1.1" file="proteins.hmmscan.22Gv1.1" ftype="tabular" compare="contains"/>
                 <element name="proteins.hmmscan.22Gv1.1.bestOrthos" file="proteins.hmmscan.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
             </output_collection>
+            <output_collection name="output_orthogroups_fasta" type="list">
+                <element name="20.faa" file="20.faa" ftype="fasta"/>
+                <element name="20.fna" file="20.fna" ftype="fasta"/>
+                <element name="3494.faa" file="3494.faa" ftype="fasta"/>
+                <element name="3494.fna" file="3494.fna" ftype="fasta"/>
+                <element name="3722.faa" file="3722.faa" ftype="fasta"/>
+                <element name="3722.fna" file="3722.fna" ftype="fasta"/>
+                <element name="38889.faa" file="38889.faa" ftype="fasta"/>
+                <element name="38889.fna" file="38889.fna" ftype="fasta"/>
+                <element name="39614.faa" file="39614.faa" ftype="fasta"/>
+                <element name="39614.fna" file="39614.fna" ftype="fasta"/>
+                <element name="5235.faa" file="5235.faa" ftype="fasta"/>
+                <element name="5235.fna" file="5235.fna" ftype="fasta"/>
+            </output_collection>
         </test>
     </tests>
     <help>