# HG changeset patch
# User yating-l
# Date 1471113909 14400
# Node ID 9a7a53f902e74197f8597e8265ad474ea6962c18
# Parent  ba64ea834baf4f505caf233a41e440936ecccad3
planemo upload commit 912f9f63cf6961808344617d270789903e650025-dirty

diff -r ba64ea834baf -r 9a7a53f902e7 error.txt
--- a/error.txt	Fri Aug 12 18:57:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
-scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
diff -r ba64ea834baf -r 9a7a53f902e7 out
--- a/out	Fri Aug 12 18:57:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
-scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
diff -r ba64ea834baf -r 9a7a53f902e7 snap.xml
--- a/snap.xml	Fri Aug 12 18:57:05 2016 -0400
+++ b/snap.xml	Sat Aug 13 14:45:09 2016 -0400
@@ -57,7 +57,7 @@
             <option value="Os.hmm">Os</option>
         </param>
         <param name="proteins" type="select" label="Create FASTA file of proteins">
-            <option value=>No</option>
+            <option value="">No</option>
             <option value="-aa">Yes</option>
         </param>
         <param name="transcripts" type="select" label="Create FASTA file of transcripts">
diff -r ba64ea834baf -r 9a7a53f902e7 test-data/thale.gff
--- a/test-data/thale.gff	Fri Aug 12 18:57:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-At1g01040.0	SNAP	Einit	1007	1954	85.269	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	2024	2137	8.926	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	2234	2444	20.788	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	2523	2917	35.162	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	3006	3225	34.428	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	3307	3479	14.790	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	3563	3685	4.678	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	3774	3934	10.179	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	4025	4258	25.991	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	4344	4506	4.289	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	4581	4763	28.696	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	4854	5015	15.217	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Exon	5100	5195	23.205	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Eterm	5285	5917	45.878	+	.	At1g01040.0-snap.1
-At1g01040.0	SNAP	Einit	6086	6144	6.596	+	.	At1g01040.0-snap.2
-At1g01040.0	SNAP	Exon	6190	6287	22.495	+	.	At1g01040.0-snap.2
-At1g01040.0	SNAP	Exon	6372	6562	17.809	+	.	At1g01040.0-snap.2
-At1g01040.0	SNAP	Exon	6642	6803	16.407	+	.	At1g01040.0-snap.2
-At1g01040.0	SNAP	Exon	6828	7547	69.159	+	.	At1g01040.0-snap.2
-At1g01040.0	SNAP	Exon	7629	7793	40.262	+	.	At1g01040.0-snap.2
-At1g01040.0	SNAP	Exon	7892	8298	46.310	+	.	At1g01040.0-snap.2
-At1g01040.0	SNAP	Eterm	8384	8561	17.079	+	.	At1g01040.0-snap.2
diff -r ba64ea834baf -r 9a7a53f902e7 test.txt
--- a/test.txt	Fri Aug 12 18:57:05 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-##gff-version 3
-At1g01040.0	SNAP	gene	1007	5917	.	+	.	ID=At1g01040.0-snap.1
-At1g01040.0	SNAP	mRNA	1007	5917	.	+	.	ID=mRNA_At1g01040.0-snap.1;Parent=At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	1007	1954	85.269	+	0	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	2024	2137	8.926	+	0	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	2234	2444	20.788	+	0	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	2523	2917	35.162	+	2	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	3006	3225	34.428	+	0	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	3307	3479	14.790	+	2	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	3563	3685	4.678	+	0	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	3774	3934	10.179	+	0	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	4025	4258	25.991	+	1	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	4344	4506	4.289	+	1	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	4581	4763	28.696	+	0	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	4854	5015	15.217	+	0	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	5100	5195	23.205	+	0	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	CDS	5285	5917	45.878	+	0	Parent=mRNA_At1g01040.0-snap.1
-At1g01040.0	SNAP	gene	6086	8561	.	+	.	ID=At1g01040.0-snap.2
-At1g01040.0	SNAP	mRNA	6086	8561	.	+	.	ID=mRNA_At1g01040.0-snap.2;Parent=At1g01040.0-snap.2
-At1g01040.0	SNAP	CDS	6086	6144	6.596	+	0	Parent=mRNA_At1g01040.0-snap.2
-At1g01040.0	SNAP	CDS	6190	6287	22.495	+	1	Parent=mRNA_At1g01040.0-snap.2
-At1g01040.0	SNAP	CDS	6372	6562	17.809	+	2	Parent=mRNA_At1g01040.0-snap.2
-At1g01040.0	SNAP	CDS	6642	6803	16.407	+	0	Parent=mRNA_At1g01040.0-snap.2
-At1g01040.0	SNAP	CDS	6828	7547	69.159	+	0	Parent=mRNA_At1g01040.0-snap.2
-At1g01040.0	SNAP	CDS	7629	7793	40.262	+	0	Parent=mRNA_At1g01040.0-snap.2
-At1g01040.0	SNAP	CDS	7892	8298	46.310	+	0	Parent=mRNA_At1g01040.0-snap.2
-At1g01040.0	SNAP	CDS	8384	8561	17.079	+	1	Parent=mRNA_At1g01040.0-snap.2