--- a/orthofinder_only_groups.xml	Mon Aug 17 12:59:19 2020 -0400
+++ b/orthofinder_only_groups.xml	Mon May 03 08:51:01 2021 +0000
@@ -1,4 +1,4 @@
-<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@">
+<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>finds orthogroups in a set of proteomes</description>
     <macros>
         <import>macros.xml</import>
@@ -163,7 +163,7 @@
             <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>
+            <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" >
             <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
@@ -199,7 +199,7 @@
     </outputs>
     <tests>
         <!-- no trees + diamond + input files have no extension fasta/faa/fa -->
-        <test>
+        <test expect_num_outputs="6">
             <conditional name="init">
                 <param name="start" value="fasta" />
                 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" />
@@ -257,7 +257,7 @@
             </output>
         </test>
         <!-- no trees + diamond + input files have extension fasta/faa/fa -->
-        <test>
+        <test expect_num_outputs="6">
             <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" />
@@ -315,7 +315,7 @@
             </output>
         </test>
         <!-- no trees + diamond + input files have extension fasta/faa/fa + keep blast out -->
-        <test>
+        <test expect_num_outputs="10">
             <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" />
@@ -377,7 +377,7 @@
             <output_collection name="wdblast" type="list" count="16"/>
         </test>
         <!-- no trees + blast + input files have extension fasta/faa/fa-->
-        <test>
+        <test expect_num_outputs="6">
             <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" />
@@ -436,7 +436,7 @@
             </output>
         </test>
         <!-- no trees + uploaded blast-->
-        <test>
+        <test expect_num_outputs="6">
             <conditional name="init">
                 <param name="start" value="blast" />
                 <param name="input_blast_out">
@@ -482,7 +482,7 @@
             <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/>
         </test>
         <!-- full mode + diamond + input files have extension fasta/faa/fa -->
-        <test>
+        <test expect_num_outputs="9">
             <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" />
@@ -540,10 +540,9 @@
             </output>
             <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/>
             <output_collection name="genetrees" type="list" count="0"/>
-            <output_collection name="resolved_trees" type="list" count="0"/>
         </test>
         <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications -->
-        <test>
+        <test expect_num_outputs="14">
             <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" />
@@ -609,7 +608,7 @@
             <output_collection name="resolved_trees" type="list" count="325"/>
         </test>
         <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
-        <test>
+        <test expect_num_outputs="6">
             <conditional name="init">
                 <param name="start" value="fasta" />
                 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" />
@@ -672,7 +671,7 @@
             </output>
         </test>
         <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
-        <test>
+        <test expect_num_outputs="9">
             <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" />