--- a/featurecounts.xml	Thu Mar 02 12:50:54 2023 +0000
+++ b/featurecounts.xml	Sat Sep 09 21:18:37 2023 +0000
@@ -2,7 +2,7 @@
     <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
     <macros>
         <token name="@TOOL_VERSION@">2.0.3</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
 
         <macro name="conditional_gff_opions">
             <param name="gff_feature_type" type="text" value="exon" argument="-t" label="GFF feature type filter" help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default."/>
@@ -137,7 +137,7 @@
         <param name="alignment"
                type="data"
                multiple="false"
-               format="bam,sam"
+               format="unsorted.bam,bam,sam"
                label="Alignment file"
                help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?">
         </param>
@@ -487,7 +487,7 @@
     </outputs>
     <tests>
         <test expect_num_outputs="3">
-            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/>
+            <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
             <param name="anno_select" value="history"/>
             <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
             <param name="format" value="tabdel_medium"/>
@@ -500,7 +500,7 @@
             </output>
         </test>
         <test expect_num_outputs="3">
-            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/>
+            <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
             <param name="anno_select" value="history"/>
             <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
             <param name="format" value="tabdel_full"/>
@@ -516,7 +516,7 @@
             </output>
         </test>
         <test expect_num_outputs="4">
-            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/>
+            <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
             <param name="anno_select" value="history"/>
             <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
             <param name="format" value="tabdel_short"/>
@@ -534,7 +534,7 @@
         </test>
         <!-- Ensure featureCounts built-in annotation works -->
         <test expect_num_outputs="3">
-            <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/>
+            <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/>
             <param name="anno_select" value="builtin"/>
             <param name="format" value="tabdel_short"/>
             <conditional name="pe_parameters">
@@ -551,7 +551,7 @@
         </test>
         <!-- Ensure fragment counting works -->
         <test expect_num_outputs="3">
-            <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/>
+            <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/>
             <param name="anno_select" value="builtin"/>
             <param name="format" value="tabdel_short"/>
             <conditional name="pe_parameters">
@@ -568,7 +568,7 @@
         </test>
         <!-- Ensure cached GTFs work -->
         <test expect_num_outputs="3">
-            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/>
+            <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
             <param name="anno_select" value="cached"/>
             <param name="format" value="tabdel_medium"/>
             <param name="include_feature_length_file" value="true"/>
@@ -580,7 +580,7 @@
             </output>
         </test>
         <!-- Ensure BAM output works -->
-        <test>
+        <test expect_num_outputs="3">
             <param name="alignment" value="subset.sorted.bam" ftype="bam"/>
             <param name="anno_select" value="history"/>
             <param name="reference_gene_sets" value="small.gtf" ftype="gtf"/>
@@ -588,6 +588,10 @@
                 <param name="R" value="true"/>
             </section>
             <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/>
+            <output name="output_short" file="subset.sorted.featurecounts_short.tab">
+                <metadata name="column_names" value="Geneid,subset.sorted.bam"/>
+            </output>
+            <output name="output_summary" file="subset.sorted.featurecounts_summary.tab"/>
         </test>
     </tests>
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subset.sorted.featurecounts_short.tab	Sat Sep 09 21:18:37 2023 +0000
@@ -0,0 +1,1390 @@
+Geneid	subset.sorted.bam
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subset.sorted.featurecounts_summary.tab	Sat Sep 09 21:18:37 2023 +0000
@@ -0,0 +1,15 @@
+Status	subset.sorted.bam
+Assigned	14
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+Unassigned_FragmentLength	0
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+Unassigned_Secondary	0
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+Unassigned_Overlapping_Length	0
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