diff --git a/t/scripts_output.t b/t/scripts_output.t
index d5da47ec..4a8afdcb 100644
--- a/t/scripts_output.t
+++ b/t/scripts_output.t
@@ -505,7 +505,23 @@ unlink $outtmp;
 
 # --------check agat_sp_flag_short_introns.pl-------------
 
-# XXX
+$script = $script_prefix."bin/agat_sp_flag_short_introns.pl";
+$result = "$output_folder/agat_sp_flag_short_introns_1.gff";
+system(" $script --gff $input_folder/agat_sp_flag_short_introns.gff -o $outtmp 2>&1 1>/dev/null");
+#run test
+ok( system("diff $result $outtmp") == 0, "output $script");
+unlink $outtmp;
+unlink $outprefix."_report.txt";
+
+# --------check agat_sp_flag_short_introns_ebi.pl-------------
+
+$script = $script_prefix."bin/agat_sp_flag_short_introns_ebi.pl";
+$result = "$output_folder/agat_sp_flag_short_introns_ebi_1.gff";
+system(" $script --gff $input_folder/agat_sp_flag_short_introns_ebi.gff -o $outtmp 2>&1 1>/dev/null");
+#run test
+ok( system("diff $result $outtmp") == 0, "output $script");
+unlink $outtmp;
+unlink $outprefix."_report.txt";
 
 # --------check agat_sp_flag_premature_stop_codons.pl-------------
 # I use result from another test because it shifted the annotation location, that allows to create pseudogenes because I use the original fasta not shifted
diff --git a/t/scripts_output/in/agat_sp_flag_short_introns.gff b/t/scripts_output/in/agat_sp_flag_short_introns.gff
new file mode 100644
index 00000000..a663e65a
--- /dev/null
+++ b/t/scripts_output/in/agat_sp_flag_short_introns.gff
@@ -0,0 +1,17 @@
+##gff-version 3
+scaffold_4	AGAT	gene	8631766	8635584	.	+	.	ID=gene28773;description=Hypothetical protein | no eggnog hit
+scaffold_4	Liftoff	mRNA	8631766	8635584	.	+	.	ID=gene28773.t1;Parent=gene28773;description=Hypothetical protein | no eggnog hit
+scaffold_4	Liftoff	exon	8631766	8634966	.	+	.	ID=gene28773.t1.exon1;Parent=gene28773.t1
+scaffold_4	Liftoff	exon	8634968	8635584	.	+	.	ID=gene28773.t1.exon2;Parent=gene28773.t1
+scaffold_4	Liftoff	CDS	8632667	8632951	.	+	0	ID=gene28773.t1.cds1;Parent=gene28773.t1
+scaffold_4	AGAT	five_prime_UTR	8631766	8632666	.	+	.	ID=agat-five_prime_utr-1269;Parent=gene28773.t1
+scaffold_4	Liftoff	intron	8634967	8634967	.	+	.	ID=intron_added-90678;Parent=gene28773.t1
+scaffold_4	AGAT	three_prime_UTR	8632952	8634966	.	+	.	ID=agat-three_prime_utr-854;Parent=gene28773.t1
+scaffold_4	AGAT	three_prime_UTR	8634968	8635584	.	+	.	ID=agat-three_prime_utr-855;Parent=gene28773.t1
+scaffold_4	AUGUSTUS	gene	8720203	8721055	.	-	.	ID=gene28774;description=F-box kelch-repeat protein
+scaffold_4	AUGUSTUS	mRNA	8720203	8721055	0.53	-	.	ID=gene28774.t1;Parent=gene28774;description=F-box kelch-repeat protein
+scaffold_4	AUGUSTUS	exon	8720203	8720819	.	-	.	ID=gene28774.t1.exon1;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	exon	8720887	8721055	.	-	.	ID=gene28774.t1.exon2;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	CDS	8720203	8720819	.	-	2	ID=gene28774.t1.cds1;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	CDS	8720887	8721055	.	-	0	ID=gene28774.t1.cds2;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	intron	8720820	8720886	.	-	.	ID=intron_added-90679;Parent=gene28774.t1
\ No newline at end of file
diff --git a/t/scripts_output/in/agat_sp_flag_short_introns_ebi.gff b/t/scripts_output/in/agat_sp_flag_short_introns_ebi.gff
new file mode 100644
index 00000000..ad50c6cd
--- /dev/null
+++ b/t/scripts_output/in/agat_sp_flag_short_introns_ebi.gff
@@ -0,0 +1,18 @@
+##gff-version 3
+scaffold_4	AGAT	gene	8631766	8635584	.	+	.	ID=gene28773;description=Hypothetical protein | no eggnog hit
+scaffold_4	Liftoff	mRNA	8631766	8635584	.	+	.	ID=gene28773.t1;Parent=gene28773;description=Hypothetical protein | no eggnog hit
+scaffold_4	Liftoff	exon	8631766	8634966	.	+	.	ID=gene28773.t1.exon1;Parent=gene28773.t1
+scaffold_4	Liftoff	exon	8634968	8635584	.	+	.	ID=gene28773.t1.exon2;Parent=gene28773.t1
+scaffold_4	Liftoff	CDS	8632667	8632951	.	+	0	ID=gene28773.t1.cds1;Parent=gene28773.t1
+scaffold_4	Liftoff	CDS	8632955	8633056	.	+	0	ID=gene28773.t1.cds1;Parent=gene28773.t1
+scaffold_4	AGAT	five_prime_UTR	8631766	8632666	.	+	.	ID=agat-five_prime_utr-1269;Parent=gene28773.t1
+scaffold_4	Liftoff	intron	8634967	8634967	.	+	.	ID=intron_added-90678;Parent=gene28773.t1
+scaffold_4	AGAT	three_prime_UTR	8632952	8634966	.	+	.	ID=agat-three_prime_utr-854;Parent=gene28773.t1
+scaffold_4	AGAT	three_prime_UTR	8634968	8635584	.	+	.	ID=agat-three_prime_utr-855;Parent=gene28773.t1
+scaffold_4	AUGUSTUS	gene	8720203	8721055	.	-	.	ID=gene28774;description=F-box kelch-repeat protein
+scaffold_4	AUGUSTUS	mRNA	8720203	8721055	0.53	-	.	ID=gene28774.t1;Parent=gene28774;description=F-box kelch-repeat protein
+scaffold_4	AUGUSTUS	exon	8720203	8720819	.	-	.	ID=gene28774.t1.exon1;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	exon	8720887	8721055	.	-	.	ID=gene28774.t1.exon2;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	CDS	8720203	8720819	.	-	2	ID=gene28774.t1.cds1;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	CDS	8720887	8721055	.	-	0	ID=gene28774.t1.cds2;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	intron	8720820	8720886	.	-	.	ID=intron_added-90679;Parent=gene28774.t1
\ No newline at end of file
diff --git a/t/scripts_output/out/agat_sp_flag_short_introns_1.gff b/t/scripts_output/out/agat_sp_flag_short_introns_1.gff
new file mode 100644
index 00000000..05f61499
--- /dev/null
+++ b/t/scripts_output/out/agat_sp_flag_short_introns_1.gff
@@ -0,0 +1,17 @@
+##gff-version 3
+scaffold_4	AGAT	gene	8631766	8635584	.	+	.	ID=gene28773;description=Hypothetical protein | no eggnog hit;short_intron=2
+scaffold_4	Liftoff	mRNA	8631766	8635584	.	+	.	ID=gene28773.t1;Parent=gene28773;description=Hypothetical protein | no eggnog hit;short_intron=2
+scaffold_4	Liftoff	exon	8631766	8634966	.	+	.	ID=gene28773.t1.exon1;Parent=gene28773.t1;short_intron=2
+scaffold_4	Liftoff	exon	8634968	8635584	.	+	.	ID=gene28773.t1.exon2;Parent=gene28773.t1;short_intron=2
+scaffold_4	Liftoff	CDS	8632667	8632951	.	+	0	ID=gene28773.t1.cds1;Parent=gene28773.t1;short_intron=2
+scaffold_4	AGAT	five_prime_UTR	8631766	8632666	.	+	.	ID=agat-five_prime_utr-1269;Parent=gene28773.t1;short_intron=2
+scaffold_4	Liftoff	intron	8634967	8634967	.	+	.	ID=intron_added-90678;Parent=gene28773.t1;short_intron=2
+scaffold_4	AGAT	three_prime_UTR	8632952	8634966	.	+	.	ID=agat-three_prime_utr-854;Parent=gene28773.t1;short_intron=2
+scaffold_4	AGAT	three_prime_UTR	8634968	8635584	.	+	.	ID=agat-three_prime_utr-855;Parent=gene28773.t1;short_intron=2
+scaffold_4	AUGUSTUS	gene	8720203	8721055	.	-	.	ID=gene28774;description=F-box kelch-repeat protein
+scaffold_4	AUGUSTUS	mRNA	8720203	8721055	0.53	-	.	ID=gene28774.t1;Parent=gene28774;description=F-box kelch-repeat protein
+scaffold_4	AUGUSTUS	exon	8720203	8720819	.	-	.	ID=gene28774.t1.exon1;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	exon	8720887	8721055	.	-	.	ID=gene28774.t1.exon2;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	CDS	8720203	8720819	.	-	2	ID=gene28774.t1.cds1;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	CDS	8720887	8721055	.	-	0	ID=gene28774.t1.cds2;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	intron	8720820	8720886	.	-	.	ID=intron_added-90679;Parent=gene28774.t1
diff --git a/t/scripts_output/out/agat_sp_flag_short_introns_ebi_1.gff b/t/scripts_output/out/agat_sp_flag_short_introns_ebi_1.gff
new file mode 100644
index 00000000..523a2ac6
--- /dev/null
+++ b/t/scripts_output/out/agat_sp_flag_short_introns_ebi_1.gff
@@ -0,0 +1,18 @@
+##gff-version 3
+scaffold_4	AGAT	gene	8631766	8635584	.	+	.	ID=gene28773;description=Hypothetical protein | no eggnog hit;pseudo=4
+scaffold_4	Liftoff	mRNA	8631766	8635584	.	+	.	ID=gene28773.t1;Parent=gene28773;description=Hypothetical protein | no eggnog hit;pseudo=4
+scaffold_4	Liftoff	exon	8631766	8634966	.	+	.	ID=gene28773.t1.exon1;Parent=gene28773.t1;pseudo=4
+scaffold_4	Liftoff	exon	8634968	8635584	.	+	.	ID=gene28773.t1.exon2;Parent=gene28773.t1;pseudo=4
+scaffold_4	Liftoff	CDS	8632667	8632951	.	+	0	ID=gene28773.t1.cds1;Parent=gene28773.t1;pseudo=4
+scaffold_4	Liftoff	CDS	8632955	8633056	.	+	0	ID=gene28773.t1.cds1;Parent=gene28773.t1;pseudo=4
+scaffold_4	AGAT	five_prime_UTR	8631766	8632666	.	+	.	ID=agat-five_prime_utr-1269;Parent=gene28773.t1;pseudo=4
+scaffold_4	Liftoff	intron	8634967	8634967	.	+	.	ID=intron_added-90678;Parent=gene28773.t1;pseudo=4
+scaffold_4	AGAT	three_prime_UTR	8632952	8634966	.	+	.	ID=agat-three_prime_utr-854;Parent=gene28773.t1;pseudo=4
+scaffold_4	AGAT	three_prime_UTR	8634968	8635584	.	+	.	ID=agat-three_prime_utr-855;Parent=gene28773.t1;pseudo=4
+scaffold_4	AUGUSTUS	gene	8720203	8721055	.	-	.	ID=gene28774;description=F-box kelch-repeat protein
+scaffold_4	AUGUSTUS	mRNA	8720203	8721055	0.53	-	.	ID=gene28774.t1;Parent=gene28774;description=F-box kelch-repeat protein
+scaffold_4	AUGUSTUS	exon	8720203	8720819	.	-	.	ID=gene28774.t1.exon1;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	exon	8720887	8721055	.	-	.	ID=gene28774.t1.exon2;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	CDS	8720203	8720819	.	-	2	ID=gene28774.t1.cds1;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	CDS	8720887	8721055	.	-	0	ID=gene28774.t1.cds2;Parent=gene28774.t1
+scaffold_4	AUGUSTUS	intron	8720820	8720886	.	-	.	ID=intron_added-90679;Parent=gene28774.t1