--- a/orthofinder_only_groups.xml	Tue Oct 24 06:40:40 2017 -0400
+++ b/orthofinder_only_groups.xml	Sun Dec 03 04:30:59 2017 -0500
@@ -1,5 +1,5 @@
 <tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="1.1.4">
-    <description>finds orthogroups in a set of proteomes</description>  
+    <description>finds orthogroups in a set of proteomes</description>
     <requirements>
         <requirement type="package" version="1.1.4">orthofinder</requirement>
     </requirements>
@@ -9,7 +9,7 @@
         #if $init.start=="fasta":
             #set $infiles = ""
             #for $input in $init.input_fasta
-                ln -s '$input' '$input.element_identifier' &&
+                ln -s '$input' '${input.element_identifier}.fasta' &&
                 #set $infiles = $infiles + str($input.element_identifier) + ","
             #end for
             #set $infiles = $infiles[:-1]
@@ -106,6 +106,59 @@
         </data>
     </outputs>
     <tests>
+        <!-- test orthofinder -f . -og when input files has no extension fasta/faa/fa ... -->
+        <test>
+            <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" />
+                <param name="keepblastout" value="no" />
+            </conditional>
+            <param name="inflation" value="1.5" />
+            <output name="specs_overlap">
+                <assert_contents>
+                    <has_text text="AcAcaud_trinity"/>
+                    <has_text text="AmAmphi_trinity"/>
+                    <has_text text="ApApomp_trinity"/>
+                    <has_text text="AsAsp1_trinity"/>
+                    <has_n_columns n="5"/>
+                </assert_contents>
+            </output>
+            <output name="unassigned_genes">
+                <assert_contents>
+                    <has_text text="AcAcaud_trinity"/>
+                    <has_text text="AmAmphi_trinity"/>
+                    <has_text text="ApApomp_trinity"/>
+                    <has_text text="AsAsp1_trinity"/>
+                    <has_n_columns n="5"/>
+                </assert_contents>
+            </output>
+            <output name="stat_overall">
+                <assert_contents>
+                    <has_text text="Number of genes in orthogroups"/>
+                    <has_text text="Number of unassigned genes"/>
+                    <has_text text="Percentage of orthogroups"/>
+                    <has_text text="Number of orthogroups"/>
+                    <has_text text="Number of genes"/>
+                    <has_text text="G50 (assigned genes)"/>
+                    <has_text text="G50 (all genes)"/>
+                    <has_text text="O50 (assigned genes)"/>
+                    <has_text text="O50 (all genes)"/>
+                </assert_contents>
+            </output>
+            <output name="stat_specs">
+                <assert_contents>
+                    <has_text text="AcAcaud_trinity"/>
+                    <has_text text="AmAmphi_trinity"/>
+                    <has_text text="ApApomp_trinity"/>
+                    <has_text text="AsAsp1_trinity"/>
+                    <has_text text="Number of genes per-species in orthogroup"/>
+                    <has_text text="Percentage of orthogroups"/>
+                    <has_text text="Number of orthogroups"/>
+                    <has_text text="Number of genes"/>
+                    <has_n_columns n="5"/>
+                </assert_contents>
+            </output>
+        </test>
         <!-- test orthofinder -f -og -->
         <test>
             <conditional name="init">
@@ -211,7 +264,6 @@
                     <has_n_columns n="5"/>
                 </assert_contents>
             </output>
-            <output name="SpeciesIDs" value="inputs/blastids/SpeciesIDs.txt" />
             <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" />
             <output_collection name="wdfasta" type="list" count="4"/>
             <output_collection name="wdblast" type="list" count="16"/>
@@ -260,7 +312,7 @@
             <output name="stat_overall" value="results_fromblast/Statistics_Overall.csv" lines_diff="2"/>
             <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.csv"/>
         </test>
-    </tests>    
+    </tests>
     <help>
 ======================
 OrthoFinder OnlyGroups