# HG changeset patch
# User iuc
# Date 1754912532 0
# Node ID b6ec80429d5436cd879bbb1de7c508bdc43982da
# Parent  b3d25fae538911d395f14a484066571bcd1eea5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 3753e5e77bcc883c92e06ae1d5bcb21eab150f35

diff -r b3d25fae5389 -r b6ec80429d54 macros.xml
--- a/macros.xml	Mon Jan 15 10:18:14 2024 +0000
+++ b/macros.xml	Mon Aug 11 11:42:12 2025 +0000
@@ -1,11 +1,52 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">2.5.5</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">24.0</token>
 
     <xml name="citations">
         <citations>
             <citation type="doi">10.1186/s13059-015-0721-2</citation>
         </citations>
     </xml>
+    <xml name="output_selector_minimal">
+        <param name="output_selector" type="select" optional="false" multiple="true" label="Outputs">
+            <yield/>
+            <!-- Comparative_Genomics_Statistics -->
+            <option value="specs_overlap" selected="true">Species overlaps</option>
+            <option value="stat_overall" selected="true">Statistics Overall</option>
+            <option value="stat_specs" selected="true">Statistics per Species</option>
+            <!-- Orthogroups results (deprecated) -->
+            <option value="orthogroups">Orthogroups (deprecated)</option>
+            <option value="orthogroups_legacy">Orthogroups - legacy format (deprecated)</option>
+            <option value="orthogroups_unassigned_genes">Orthogroups - with unassigned genes (deprecated)</option>
+
+        </param>
+    </xml>
+
+    <xml name="output_selector_full">
+        <expand macro="output_selector_minimal">
+                <option value="phylogenetic_hierarchical_orthogroups" selected="true">Phylogenetic Hierarchical Orthogroups Directory</option>
+                <!-- Orthologues results -->
+                <option value="orthologues" selected="true">Orthologs</option>
+                <option value="orthologues_per_species">Orthologs per species</option>
+                <!-- gene trees -->
+                <option value="gene_trees" selected="true">Gene Trees</option>
+                <option value="resolved_gene_trees">Resolved Gene Trees</option>
+                <!-- Species Trees Directory -->
+                <option value="species_tree" selected="true">Species Tree</option>
+                <option value="species_tree_node_labels" selected="true">Species Trees with nodes labels</option>
+                <!-- Gene_Duplication_Events -->
+                <option value="speciestree_gene_duplication_0.5_support">Species tree with gene duplications (support>=0.5)</option>
+                <option value="duplications">Duplications</option>
+                <!-- Comparative_Genomics_Statistics -->
+                <option value="duplications_per_orthogroup">Duplications per Orthogroup</option>
+                <option value="duplications_per_species_tree_node">Duplications per Species Tree Node</option>
+                <option value="orthologuesstats_many_to_many">OrthologuesStats many-to-many</option>
+                <option value="orthologuesstats_one_to_many">OrthologuesStats one-to-many</option>
+                <option value="orthologuesstats_many_to_one">OrthologuesStats many-to-one</option>
+                <option value="orthologuesstats_total" selected="true">OrthologuesStats Total</option>
+        </expand>
+    </xml>
+
 </macros>
diff -r b3d25fae5389 -r b6ec80429d54 orthofinder_only_groups.xml
--- a/orthofinder_only_groups.xml	Mon Jan 15 10:18:14 2024 +0000
+++ b/orthofinder_only_groups.xml	Mon Aug 11 11:42:12 2025 +0000
@@ -1,4 +1,4 @@
-<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>finds orthogroups in a set of proteomes</description>
     <macros>
         <import>macros.xml</import>
@@ -116,13 +116,11 @@
                 <param name="seqIDs" type="data" format="txt" label="Select the SequencesIds file" help="SequencesIDs.txt file from the blast output files of a previous OrthoFinder run."/>
             </when>
         </conditional>
-
         <conditional name="trees">
             <param name="run_mode" type="select" label="Orthofinder run mode">
                 <option value="full" selected="true">Full run (including gene trees)</option>
                 <option value="-og">Stop after inferring orthogroups (no gene trees)</option>
             </param>
-
             <when value="full">
                 <conditional name="tree_method">
                     <param name="method" type="select" label="Method for gene tree inference">
@@ -145,69 +143,126 @@
 
                     <when value="dendroblast"/>
                 </conditional>
+                <expand macro="output_selector_full"/>
             </when>
-
-            <when value="-og"/>
+            <when value="-og">
+                <expand macro="output_selector_minimal"/>
+            </when>
         </conditional>
-
         <param argument="-I" name="inflation" type="float" value="1.5" label="Inflation parameter" help="Modify inflation parameter for MCL. Not recommended." />
-        <param name="output_duplications" type="boolean" checked="false" label="Generate output about gene duplication events"/>
     </inputs>
     <outputs>
-        <!-- Orthogroups results -->
-        <data format="txt" name="orthogroups1" label="OrthoFinder on ${on_string}: orthogroups (txt)" from_work_dir="results/Orthogroups/Orthogroups.txt" />
-        <data format="tsv" name="orthogroups2" label="OrthoFinder on ${on_string}: orthogroups (tsv)" from_work_dir="results/Orthogroups/Orthogroups.tsv" />
-        <data format="tsv" name="hogs" label="OrthoFinder on ${on_string}: hierarchical orthogroups (tsv)" from_work_dir="results/Phylogenetic_Hierarchical_Orthogroups/N0.tsv" >
+        <collection name="hogs" type="list" label="${tool.name} on ${on_string}: hierarchical orthogroups (tsv)">
+            <discover_datasets pattern="__name_and_ext__" directory="results/Phylogenetic_Hierarchical_Orthogroups/" />
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"phylogenetic_hierarchical_orthogroups" in trees['output_selector']</filter>
+        </collection>
+
+        <!-- Orthologues results -->
+        <collection name="orthologues" type="list:list" label="${tool.name} on ${on_string}: Orthologues (tsv)">
+            <discover_datasets pattern="Orthologues_(?P&lt;identifier_0&gt;.+)/(?P&lt;identifier_1&gt;.+)\.tsv" directory="results/Orthologues/" match_relative_path="true" format="tsv" recurse="true"/>
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"orthologues" in trees['output_selector']</filter>
+        </collection>
+        <collection name="orthologues_per_species" type="list" label="${tool.name} on ${on_string}: Orthologues per species(tsv)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="results/Orthologues/" format="tsv"/>
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"orthologues_per_species" in trees['output_selector']</filter>
+        </collection>
+
+        <!-- Orthogroups results (deprecated) -->
+        <data format="txt" name="orthogroups1" label="${tool.name} on ${on_string}: orthogroups (txt)" from_work_dir="results/Orthogroups/Orthogroups.txt">
+            <filter>"orthogroups" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="orthogroups2" label="${tool.name} on ${on_string}: orthogroups (tsv)" from_work_dir="results/Orthogroups/Orthogroups.tsv">
+            <filter>"orthogroups_legacy" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="unassigned_genes" label="${tool.name} on ${on_string}: unassigned genes" from_work_dir="results/Orthogroups/Orthogroups_UnassignedGenes.tsv">
+            <filter>"orthogroups_unassigned_genes" in trees['output_selector']</filter>
+        </data>
+
+        <!-- gene trees -->
+        <collection name="genetrees" type="list" label="${tool.name} on ${on_string}: gene trees">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="results/Gene_Trees" format="newick" />
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"gene_trees" in trees['output_selector']</filter>
+        </collection>
+        <collection name="resolved_genetrees" type="list" label="${tool.name} on ${on_string}: resolved gene trees">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="results/Resolved_Gene_Trees" format="newick" />
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"resolved_gene_trees" in trees['output_selector']</filter>
+        </collection>
+
+        <!-- Species Trees Directory -->
+        <data format="newick" name="species_tree" label="${tool.name} on ${on_string}: species tree" from_work_dir="results/Species_Tree/SpeciesTree_rooted.txt">
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"species_tree" in trees['output_selector']</filter>
+        </data>
+        <data format="newick" name="species_tree_label" label="${tool.name} on ${on_string}: species tree with node labels" from_work_dir="results/Species_Tree/SpeciesTree_rooted_node_labels.txt">
             <filter>trees['run_mode'] == "full"</filter>
+            <filter>"species_tree_node_labels" in trees['output_selector']</filter>
         </data>
-        <data format="tsv" name="specs_overlap" label="OrthoFinder on ${on_string}: species overlaps" from_work_dir="results/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv" />
-        <data format="tsv" name="unassigned_genes" label="OrthoFinder on ${on_string}: unassigned genes" from_work_dir="results/Orthogroups/Orthogroups_UnassignedGenes.tsv" />
-        <data format="tsv" name="stat_overall" label="OrthoFinder on ${on_string}: overall comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_Overall.tsv" />
-        <data format="tsv" name="stat_specs" label="OrthoFinder on ${on_string}: per species comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv" />
+
+        <!-- Comparative Genomics Statistics Directory -->
+        <data format="tsv" name="duplications_per_orthogroup" label="${tool.name} on ${on_string}: duplications per orthogroup" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv">
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"duplications_per_orthogroup" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="duplications_per_species_tree_node" label="${tool.name} on ${on_string}: duplications per species tree node" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv">
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"duplications_per_species_tree_node" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="specs_overlap" label="${tool.name} on ${on_string}: species overlaps" from_work_dir="results/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv">
+            <filter>"specs_overlap" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="orthologuesstats_many_to_many" label="${tool.name} on ${on_string}: OrthologuesStats many-to-many" from_work_dir="results/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv">
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"orthologuesstats_many_to_many" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="orthologuesstats_one_to_many" label="${tool.name} on ${on_string}: OrthologuesStats one-to-many" from_work_dir="results/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv">
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"orthologuesstats_one_to_many" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="orthologuesstats_many_to_one" label="${tool.name} on ${on_string}: OrthologuesStats many-to-one" from_work_dir="results/Comparative_Genomics_Statistics/OrthologuesStats_many-to-one">
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"orthologuesstats_many_to_one" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="orthologuesstats_total" label="${tool.name} on ${on_string}: OrthologuesStats Total" from_work_dir="results/Comparative_Genomics_Statistics/OrthologuesStats_Total.tsv">
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"orthologuesstats_total" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="stat_overall" label="${tool.name} on ${on_string}: overall comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_Overall.tsv">
+            <filter>"stat_overall" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="stat_specs" label="${tool.name} on ${on_string}: per species comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv">
+            <filter>"stat_specs" in trees['output_selector']</filter>
+        </data>
+
+        <!-- Gene_Duplication_Events -->
+        <data format="newick" name="species_tree_duplications" label="${tool.name} on ${on_string}: species tree with duplication events" from_work_dir="results/Gene_Duplication_Events/SpeciesTree_Gene_Duplications_0.5_Support.txt">
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"speciestree_gene_duplication_0.5_support" in trees['output_selector']</filter>
+        </data>
+        <data format="tsv" name="duplications" label="${tool.name} on ${on_string}: duplication events" from_work_dir="results/Gene_Duplication_Events/Duplications.tsv">
+            <filter>trees['run_mode'] == "full"</filter>
+            <filter>"duplications" in trees['output_selector']</filter>
+        </data>
 
         <!-- working directory : blast outputs-->
-        <collection name="wdblast" type="list" label="OrthoFinder on ${on_string}: blast outputs">
+        <collection name="wdblast" type="list" label="${tool.name} on ${on_string}: blast outputs">
             <discover_datasets pattern="__name_and_ext__" directory="results/WorkingDirectory/blast" />
             <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
         </collection>
-        <collection name="wdfasta" type="list" label="OrthoFinder on ${on_string}: fasta from blast" >
+        <collection name="wdfasta" type="list" label="${tool.name} on ${on_string}: fasta from blast" >
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fa" directory="results/WorkingDirectory/fa" format="fasta" />
             <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
         </collection>
-        <data format="txt" name="SpeciesIDs" label="OrthoFinder on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" >
-            <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
-        </data>
-        <data format="txt" name="SequenceIDs" label="OrthoFinder on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
+        <data format="txt" name="SpeciesIDs" label="${tool.name} on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" >
             <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
         </data>
-
-        <data format="newick" name="species_tree" label="OrthoFinder on ${on_string}: species tree" from_work_dir="results/Species_Tree/SpeciesTree_rooted.txt">
-            <filter>trees['run_mode'] == "full"</filter>
-        </data>
-        <data format="newick" name="species_tree_label" label="OrthoFinder on ${on_string}: species tree with node labels" from_work_dir="results/Species_Tree/SpeciesTree_rooted_node_labels.txt">
-            <filter>trees['run_mode'] == "full"</filter>
+        <data format="txt" name="SequenceIDs" label="${tool.name} on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
+            <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
         </data>
-        <collection name="genetrees" type="list" label="OrthoFinder on ${on_string}: gene trees">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="results/Gene_Trees" format="newick" />
-            <filter>trees['run_mode'] == "full"</filter>
-        </collection>
-
-        <data format="newick" name="species_tree_duplications" label="OrthoFinder on ${on_string}: species tree with duplication events" from_work_dir="results/Gene_Duplication_Events/SpeciesTree_Gene_Duplications_0.5_Support.txt">
-            <filter>trees['run_mode'] == "full" and output_duplications</filter>
-        </data>
-        <data format="tsv" name="duplications" label="OrthoFinder on ${on_string}: duplication events" from_work_dir="results/Gene_Duplication_Events/Duplications.tsv">
-            <filter>trees['run_mode'] == "full" and output_duplications</filter>
-        </data>
-        <data format="tsv" name="duplications_per_orthogroup" label="OrthoFinder on ${on_string}: duplications per orthogroup" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv">
-            <filter>trees['run_mode'] == "full" and output_duplications</filter>
-        </data>
-        <data format="tsv" name="duplications_per_species_tree_node" label="OrthoFinder on ${on_string}: duplications per species tree node" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv">
-            <filter>trees['run_mode'] == "full" and output_duplications</filter>
-        </data>
-        <collection name="resolved_trees" type="list" label="OrthoFinder on ${on_string}: resolved gene trees">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="results/Resolved_Gene_Trees" format="newick" />
-            <filter>trees['run_mode'] == "full" and output_duplications</filter>
-        </collection>
     </outputs>
     <tests>
         <!-- no trees + diamond + input files have no extension fasta/faa/fa -->
@@ -221,6 +276,7 @@
             </conditional>
             <conditional name="trees">
                 <param name="run_mode" value="-og" />
+                <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/>
             </conditional>
             <param name="inflation" value="1.5" />
             <output name="specs_overlap">
@@ -279,6 +335,7 @@
             </conditional>
             <conditional name="trees">
                 <param name="run_mode" value="-og" />
+                <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/>
             </conditional>
             <param name="inflation" value="1.5" />
             <output name="specs_overlap">
@@ -338,6 +395,7 @@
             </conditional>
             <conditional name="trees">
                 <param name="run_mode" value="-og" />
+                <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/>
             </conditional>
             <param name="inflation" value="1.5" />
             <output name="specs_overlap">
@@ -400,6 +458,7 @@
             </conditional>
             <conditional name="trees">
                 <param name="run_mode" value="-og" />
+                <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/>
             </conditional>
             <param name="inflation" value="1.5" />
             <output name="specs_overlap">
@@ -484,17 +543,18 @@
             </conditional>
             <conditional name="trees">
                 <param name="run_mode" value="-og" />
+                <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/>
             </conditional>
             <param name="inflation" value="1.5" />
             <output name="orthogroups1" value="results_fromblast/Orthogroups.txt"/>
             <output name="orthogroups2" value="results_fromblast/Orthogroups.tsv"/>
+            <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/>
             <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.tsv"/>
-            <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/>
             <output name="stat_overall" value="results_fromblast/Statistics_Overall.tsv" lines_diff="2"/>
             <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/>
         </test>
         <!-- full mode + diamond + input files have extension fasta/faa/fa -->
-        <test expect_num_outputs="10">
+        <test expect_num_outputs="11">
             <conditional name="init">
                 <param name="start" value="fasta" />
                 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
@@ -504,6 +564,7 @@
             </conditional>
             <conditional name="trees">
                 <param name="run_mode" value="full" />
+                <param name="output_selector" value="phylogenetic_hierarchical_orthogroups,orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,gene_trees,resolved_gene_trees,specs_overlap,stat_overall,stat_specs,species_tree,species_tree_node_labels"/>
             </conditional>
             <param name="inflation" value="1.5" />
             <output name="specs_overlap">
@@ -551,19 +612,22 @@
                 </assert_contents>
             </output>
             <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/>
-            <output_collection name="genetrees" type="list" count="0"/>
-            <output name="hogs">
-                <assert_contents>
-                    <has_text text="HOG" />
-                    <has_text text="OG" />
-                    <has_text text="Gene Tree Parent Clade" />
-                    <has_text text="Mycoplasma_agalactiae"/>
-                    <has_text text="Mycoplasma_gallisepticum"/>
-                    <has_text text="Mycoplasma_genitalium"/>
-                    <has_text text="Mycoplasma_hyopneumoniae"/>
-                    <has_n_columns n="7"/>
-                </assert_contents>
-            </output>
+            <output_collection name="genetrees" type="list" count="325"/>
+            <output_collection name="resolved_genetrees" type="list" count="325"/>
+            <output_collection name="hogs" type="list" count="3">
+                <element name="N0">
+                    <assert_contents>
+                        <has_text text="HOG" />
+                        <has_text text="OG" />
+                        <has_text text="Gene Tree Parent Clade" />
+                        <has_text text="Mycoplasma_agalactiae"/>
+                        <has_text text="Mycoplasma_gallisepticum"/>
+                        <has_text text="Mycoplasma_genitalium"/>
+                        <has_text text="Mycoplasma_hyopneumoniae"/>
+                        <has_n_columns n="7"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
         <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications -->
         <test expect_num_outputs="15">
@@ -576,9 +640,9 @@
             </conditional>
             <conditional name="trees">
                 <param name="run_mode" value="full" />
+                <param name="output_selector" value="phylogenetic_hierarchical_orthogroups,orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,gene_trees,resolved_gene_trees,duplications_per_orthogroup,duplications_per_species_tree_node,specs_overlap,stat_overall,stat_specs,species_tree,species_tree_node_labels,speciestree_gene_duplication_0.5_support,duplications"/>
             </conditional>
             <param name="inflation" value="1.5" />
-            <param name="output_duplications" value="true" />
             <output name="specs_overlap">
                 <assert_contents>
                     <has_text text="Mycoplasma_agalactiae"/>
@@ -629,21 +693,23 @@
             <output name="duplications_per_orthogroup" value="results/Duplications_per_Orthogroup.tsv" compare="sim_size"/>
             <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/>
             <output_collection name="genetrees" type="list" count="325"/>
-            <output_collection name="resolved_trees" type="list" count="325"/>
-            <output name="hogs">
-                <assert_contents>
-                    <has_text text="HOG" />
-                    <has_text text="OG" />
-                    <has_text text="Gene Tree Parent Clade" />
-                    <has_text text="Mycoplasma_agalactiae"/>
-                    <has_text text="Mycoplasma_gallisepticum"/>
-                    <has_text text="Mycoplasma_genitalium"/>
-                    <has_text text="Mycoplasma_hyopneumoniae"/>
-                    <has_n_columns n="7"/>
-                </assert_contents>
-            </output>
+            <output_collection name="resolved_genetrees" type="list" count="325"/>
+            <output_collection name="hogs" type="list" count="3">
+                <element name="N0">
+                    <assert_contents>
+                        <has_text text="HOG" />
+                        <has_text text="OG" />
+                        <has_text text="Gene Tree Parent Clade" />
+                        <has_text text="Mycoplasma_agalactiae"/>
+                        <has_text text="Mycoplasma_gallisepticum"/>
+                        <has_text text="Mycoplasma_genitalium"/>
+                        <has_text text="Mycoplasma_hyopneumoniae"/>
+                        <has_n_columns n="7"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
-        <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
+        <!-- diamond + input files have no extension fasta/faa/fa + msa -->
         <test expect_num_outputs="6">
             <conditional name="init">
                 <param name="start" value="fasta" />
@@ -654,11 +720,7 @@
             </conditional>
             <conditional name="trees">
                 <param name="run_mode" value="-og" />
-                <conditional name="tree_method">
-                    <param name="method" value="msa" />
-                    <param name="msa_program" value="muscle" />
-                    <param name="msa_tree_program" value="raxml" />
-                </conditional>
+                <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/>
             </conditional>
             <param name="inflation" value="1.5" />
             <output name="specs_overlap">
@@ -707,7 +769,7 @@
             </output>
         </test>
         <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
-        <test expect_num_outputs="10">
+        <test expect_num_outputs="12">
             <conditional name="init">
                 <param name="start" value="fasta" />
                 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
@@ -722,6 +784,7 @@
                     <param name="msa_program" value="muscle" />
                     <param name="msa_tree_program" value="raxml" />
                 </conditional>
+                <param name="output_selector" value="phylogenetic_hierarchical_orthogroups,orthologues,orthologues_per_species,orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,gene_trees,specs_overlap,stat_overall,stat_specs,species_tree,species_tree_node_labels"/>
             </conditional>
             <param name="inflation" value="1.5" />
             <output name="specs_overlap">
@@ -768,18 +831,48 @@
                     <has_n_columns n="5"/>
                 </assert_contents>
             </output>
-            <output name="hogs">
-                <assert_contents>
-                    <has_text text="HOG" />
-                    <has_text text="OG" />
-                    <has_text text="Gene Tree Parent Clade" />
-                    <has_text text="Mycoplasma_agalactiae"/>
-                    <has_text text="Mycoplasma_gallisepticum"/>
-                    <has_text text="Mycoplasma_genitalium"/>
-                    <has_text text="Mycoplasma_hyopneumoniae"/>
-                    <has_n_columns n="7"/>
-                </assert_contents>
-            </output>
+            <output_collection name="hogs" type="list" count="3">
+                <element name="N0">
+                    <assert_contents>
+                        <has_text text="HOG" />
+                        <has_text text="OG" />
+                        <has_text text="Gene Tree Parent Clade" />
+                        <has_text text="Mycoplasma_agalactiae"/>
+                        <has_text text="Mycoplasma_gallisepticum"/>
+                        <has_text text="Mycoplasma_genitalium"/>
+                        <has_text text="Mycoplasma_hyopneumoniae"/>
+                        <has_n_columns n="7"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="orthologues" type="list:list" count="4">
+                <element name="Mycoplasma_agalactiae.faa" count="3">
+                    <element name="Mycoplasma_agalactiae.faa__v__Mycoplasma_gallisepticum.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                    <element name="Mycoplasma_agalactiae.faa__v__Mycoplasma_genitalium.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                    <element name="Mycoplasma_agalactiae.faa__v__Mycoplasma_hyopneumoniae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                </element>
+                <element name="Mycoplasma_gallisepticum.faa" count="3">
+                    <element name="Mycoplasma_gallisepticum.faa__v__Mycoplasma_agalactiae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                    <element name="Mycoplasma_gallisepticum.faa__v__Mycoplasma_genitalium.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                    <element name="Mycoplasma_gallisepticum.faa__v__Mycoplasma_hyopneumoniae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                </element>
+                <element name="Mycoplasma_genitalium.faa" count="3">
+                    <element name="Mycoplasma_genitalium.faa__v__Mycoplasma_agalactiae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                    <element name="Mycoplasma_genitalium.faa__v__Mycoplasma_gallisepticum.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                    <element name="Mycoplasma_genitalium.faa__v__Mycoplasma_hyopneumoniae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                </element>
+                <element name="Mycoplasma_hyopneumoniae.faa" count="3">
+                    <element name="Mycoplasma_hyopneumoniae.faa__v__Mycoplasma_agalactiae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                    <element name="Mycoplasma_hyopneumoniae.faa__v__Mycoplasma_gallisepticum.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                    <element name="Mycoplasma_hyopneumoniae.faa__v__Mycoplasma_genitalium.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element>
+                </element>
+            </output_collection>
+            <output_collection name="orthologues_per_species" type="list" count="4">
+                <element name="Mycoplasma_agalactiae.faa"><assert_contents><has_n_columns n="4"/></assert_contents></element>
+                <element name="Mycoplasma_gallisepticum.faa"><assert_contents><has_n_columns n="4"/></assert_contents></element>
+                <element name="Mycoplasma_genitalium.faa"><assert_contents><has_n_columns n="4"/></assert_contents></element>
+                <element name="Mycoplasma_hyopneumoniae.faa"><assert_contents><has_n_columns n="4"/></assert_contents></element>
+            </output_collection>
             <assert_command>
                 <has_text text="-M 'msa'"/>
                 <has_text text="-A 'muscle'"/>
@@ -792,8 +885,7 @@
 OrthoFinder OnlyGroups
 ======================
 
-Full readme at https://github.com/davidemms/OrthoFinder/blob/master/README.md
-Summary sketch at https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf
+More information at https://orthofinder.github.io/OrthoFinder/
 
 OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format (Emms, D.M. and Kelly, S., 2015).