# HG changeset patch
# User iuc
# Date 1654815437 0
# Node ID 2e92e1929cb1f66d261ec536ba753f963f8d462d
# Parent 32c11a4b5dbf4dd53c770be91fde9cb3bf8095af
planemo upload for repository https://github.com/ogotoh/spaln commit ab06c07b81a9a6883ec58d3da22bed6e2b63d4d5
diff -r 32c11a4b5dbf -r 2e92e1929cb1 macros.xml
--- a/macros.xml Wed Feb 02 14:15:38 2022 +0000
+++ b/macros.xml Thu Jun 09 22:57:17 2022 +0000
@@ -1,3 +1,4 @@
- 2.4.7
-
\ No newline at end of file
+ 2.4.9
+ 0
+
diff -r 32c11a4b5dbf -r 2e92e1929cb1 spaln.xml
--- a/spaln.xml Wed Feb 02 14:15:38 2022 +0000
+++ b/spaln.xml Thu Jun 09 22:57:17 2022 +0000
@@ -1,4 +1,4 @@
-
+
Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.
macros.xml
diff -r 32c11a4b5dbf -r 2e92e1929cb1 test-data/output1.bed12
--- a/test-data/output1.bed12 Wed Feb 02 14:15:38 2022 +0000
+++ b/test-data/output1.bed12 Thu Jun 09 22:57:17 2022 +0000
@@ -1,2 +1,2 @@
track name=Spaln description="NP_001121846.1" useScore=1
-scaffold_1 16 10418 NP_001121846.1 355 + 16 10418 255,0,0 16 46,30,122,127,33,4,127,33,6,18,15,11,13,24,24,24, 0,288,401,7107,7546,7642,7721,7908,8278,8849,8963,9050,9959,10028,10212,10378
+scaffold_1 16 10421 NP_001121846.1 284 + 16 10421 255,0,0 16 46,30,122,127,33,4,127,33,6,18,15,11,13,24,24,27, 0,288,401,7107,7546,7642,7721,7908,8278,8849,8963,9050,9959,10028,10212,10378
diff -r 32c11a4b5dbf -r 2e92e1929cb1 test-data/output1.tabular
--- a/test-data/output1.tabular Wed Feb 02 14:15:38 2022 +0000
+++ b/test-data/output1.tabular Thu Jun 09 22:57:17 2022 +0000
@@ -1,18 +1,18 @@
# rID gID %id ExonL MisMch Unpair ref_l ref_r tgt_l tgt_r eScore IntrnL iScore Sig3/I Sig5/T # - X P DiNuc
-NP_001121846.1 scaffold_1 23.53 46 10 2 1 15 17 62 7.1 0 0.0 6.64 0.09 0 0 0 0 .
-NP_001121846.1 scaffold_1 14.29 30 8 2 16 27 305 334 0.6 242 -1.6 0.99 0.40 0 0 0 1 GT.AG
-NP_001121846.1 scaffold_1 65.85 122 14 0 28 68 418 539 20.7 83 -0.1 1.61 0.65 0 0 0 1 GT.AG
-NP_001121846.1 scaffold_1 64.29 127 15 0 69 110 7124 7250 18.7 6584 -2.5 1.45 1.77 0 0 0 0 GT.AG
-NP_001121846.1 scaffold_1 9.09 33 10 0 111 121 7563 7595 1.1 312 -0.4 0.56 0.51 0 0 0 1 GT.AG
-NP_001121846.1 scaffold_1 0.00 4 2 0 122 123 7659 7662 2.1 63 -0.7 0.78 1.38 0 0 0 1 GT.AG
-NP_001121846.1 scaffold_1 20.00 127 31 3 124 165 7738 7864 2.2 75 0.5 1.17 1.32 0 0 0 2 GT.AG
-NP_001121846.1 scaffold_1 9.09 33 10 0 166 176 7925 7957 2.6 60 0.1 0.71 0.96 0 0 0 0 GT.AG
-NP_001121846.1 scaffold_1 50.00 6 1 0 177 178 8295 8300 2.9 337 -1.0 0.88 1.07 0 0 0 0 GT.AG
-NP_001121846.1 scaffold_1 16.67 18 5 0 179 184 8866 8883 3.1 565 -0.8 1.20 1.75 0 0 0 0 GT.AG
-NP_001121846.1 scaffold_1 0.00 15 5 0 185 189 8980 8994 3.0 96 1.1 1.58 0.90 0 0 0 0 GT.AG
-NP_001121846.1 scaffold_1 0.00 11 4 0 190 193 9067 9077 2.7 72 -0.4 0.70 0.75 0 0 0 0 GT.AG
-NP_001121846.1 scaffold_1 25.00 13 3 0 194 197 9976 9988 2.8 898 -2.2 0.67 1.54 0 0 0 2 GT.AG
-NP_001121846.1 scaffold_1 37.50 24 5 0 198 205 10045 10068 2.8 56 0.4 0.77 0.51 0 0 0 0 GT.AG
-NP_001121846.1 scaffold_1 25.00 24 6 0 206 213 10229 10252 3.8 160 -0.7 1.30 1.25 0 0 0 0 GT.AG
-NP_001121846.1 scaffold_1 20.00 24 6 1 214 222 10395 10418 4.6 142 0.0 1.24 3.54 0 0 0 0 GT.AG
-@ scaffold_1 + ( 17 10418 ) NP_001121846.1 [1:222] ( 1 222 ) S: 420.1 =: 36.5 C: 97.3 T#: 135 T-: 8 B#: 0 B-: 0 X: 0 Nexn: 16 HC: 6.8
+NP_001121846.1 scaffold_1 19.05 46 10 6 1 15 17 62 7.1 0 0.0 6.64 0.09 6 2 0 0 .
+NP_001121846.1 scaffold_1 11.11 30 8 6 16 27 305 334 0.6 242 -1.6 0.99 0.40 6 1 0 1 GT.AG
+NP_001121846.1 scaffold_1 65.85 122 14 0 28 68 418 539 20.7 83 -0.1 1.61 0.65 6 1 0 1 GT.AG
+NP_001121846.1 scaffold_1 64.29 127 15 0 69 110 7124 7250 18.7 6584 -2.5 1.45 1.77 4 0 0 0 GT.AG
+NP_001121846.1 scaffold_1 9.09 33 10 0 111 121 7563 7595 1.1 312 -0.4 0.56 0.51 8 0 0 1 GT.AG
+NP_001121846.1 scaffold_1 0.00 4 2 0 122 123 7659 7662 2.1 63 -0.7 0.78 1.38 9 0 0 1 GT.AG
+NP_001121846.1 scaffold_1 17.65 127 31 9 124 165 7738 7864 2.2 75 0.5 1.17 1.32 8 0 0 2 GT.AG
+NP_001121846.1 scaffold_1 9.09 33 10 0 166 176 7925 7957 2.6 60 0.1 0.71 0.96 10 0 0 0 GT.AG
+NP_001121846.1 scaffold_1 50.00 6 1 0 177 178 8295 8300 2.9 337 -1.0 0.88 1.07 9 0 0 0 GT.AG
+NP_001121846.1 scaffold_1 16.67 18 5 0 179 184 8866 8883 3.1 565 -0.8 1.20 1.75 9 0 0 0 GT.AG
+NP_001121846.1 scaffold_1 0.00 15 5 0 185 189 8980 8994 3.0 96 1.1 1.58 0.90 9 0 0 0 GT.AG
+NP_001121846.1 scaffold_1 0.00 11 4 0 190 193 9067 9077 2.7 72 -0.4 0.70 0.75 10 0 0 0 GT.AG
+NP_001121846.1 scaffold_1 25.00 13 3 0 194 197 9976 9988 2.8 898 -2.2 0.67 1.54 10 0 0 2 GT.AG
+NP_001121846.1 scaffold_1 37.50 24 5 0 198 205 10045 10068 2.8 56 0.4 0.77 0.51 7 0 0 0 GT.AG
+NP_001121846.1 scaffold_1 25.00 24 6 0 206 213 10229 10252 3.8 160 -0.7 1.30 1.25 7 0 0 0 GT.AG
+NP_001121846.1 scaffold_1 16.67 27 6 3 214 222 10395 10421 -3.8 142 0.0 1.24 0.00 7 0 0 0 GT.AG
+@ scaffold_1 + ( 17 10421 ) NP_001121846.1 [1:222] ( 1 222 ) S: 336.1 =: 36.5 C: 97.3 T#: 135 T-: 24 B#: 119 B-: 6 X: 0 Nexn: 16 HC: 6.8
diff -r 32c11a4b5dbf -r 2e92e1929cb1 test-data/output1_gff_genes.gff3
--- a/test-data/output1_gff_genes.gff3 Wed Feb 02 14:15:38 2022 +0000
+++ b/test-data/output1_gff_genes.gff3 Thu Jun 09 22:57:17 2022 +0000
@@ -1,7 +1,7 @@
##gff-version 3
##sequence-region scaffold_1 1 59940
-scaffold_1 ALN gene 17 10418 420 + . ID=gene00001;Name=scaffold_1_5
-scaffold_1 ALN mRNA 17 10418 420 + . ID=mRNA00001;Parent=gene00001;Name=scaffold_1_5
+scaffold_1 ALN gene 17 10421 336 + . ID=gene00001;Name=scaffold_1_5
+scaffold_1 ALN mRNA 17 10421 336 + . ID=mRNA00001;Parent=gene00001;Name=scaffold_1_5
scaffold_1 ALN cds 17 62 71 + 0 ID=cds00001;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 1 15 +
scaffold_1 ALN cds 305 334 5 + 2 ID=cds00002;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 16 27 +
scaffold_1 ALN cds 418 539 207 + 2 ID=cds00003;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 28 68 +
@@ -17,4 +17,4 @@
scaffold_1 ALN cds 9976 9988 28 + 1 ID=cds00013;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 194 197 +
scaffold_1 ALN cds 10045 10068 27 + 0 ID=cds00014;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 198 205 +
scaffold_1 ALN cds 10229 10252 38 + 0 ID=cds00015;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 206 213 +
-scaffold_1 ALN cds 10395 10418 46 + 0 ID=cds00016;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +
+scaffold_1 ALN cds 10395 10421 -37 + 0 ID=cds00016;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +
diff -r 32c11a4b5dbf -r 2e92e1929cb1 test-data/output1_gff_matches.gff3
--- a/test-data/output1_gff_matches.gff3 Wed Feb 02 14:15:38 2022 +0000
+++ b/test-data/output1_gff_matches.gff3 Thu Jun 09 22:57:17 2022 +0000
@@ -15,4 +15,4 @@
scaffold_1 ALN nucleotide_to_protein_match 9976 9988 28 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 194 197 +;Gap=M4
scaffold_1 ALN nucleotide_to_protein_match 10045 10068 27 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 198 205 +;Gap=M8
scaffold_1 ALN nucleotide_to_protein_match 10229 10252 38 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 206 213 +;Gap=M8
-scaffold_1 ALN nucleotide_to_protein_match 10395 10418 46 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +;Gap=M5 I1 M3
+scaffold_1 ALN nucleotide_to_protein_match 10395 10421 -37 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +;Gap=M5 I1 M3 D1
diff -r 32c11a4b5dbf -r 2e92e1929cb1 test-data/output2.tabular
--- a/test-data/output2.tabular Wed Feb 02 14:15:38 2022 +0000
+++ b/test-data/output2.tabular Thu Jun 09 22:57:17 2022 +0000
@@ -1,7 +1,7 @@
# rID gID %id ExonL MisMch Unpair ref_l ref_r tgt_l tgt_r eScore IntrnL iScore Sig3/I Sig5/T # - X P DiNuc
-NP_001121846.1 scaffold_1 10.00 91 24 3 1 27 17 107 5.5 0 0.0 6.64 0.58 0 0 0 0 .
-NP_001121846.1 scaffold_1 65.85 122 14 0 28 68 418 539 21.2 310 -1.7 1.88 0.83 0 0 0 1 GT.AG
-NP_001121846.1 scaffold_1 64.29 127 15 0 69 110 7124 7250 18.9 6584 -3.1 1.77 1.71 0 0 0 0 GT.AG
-NP_001121846.1 scaffold_1 24.49 147 30 7 111 152 44187 44333 3.0 36936 -4.2 1.03 1.02 0 0 0 1 GT.AG
-NP_001121846.1 scaffold_1 18.75 221 52 10 153 222 44595 44815 4.8 261 -1.6 1.50 3.36 0 0 0 1 GT.AG
-@ scaffold_1 + ( 17 44815 ) NP_001121846.1 [1:222] ( 1 222 ) S: 324.7 =: 37.8 C: 98.6 T#: 135 T-: 20 B#: 0 B-: 0 X: 0 Nexn: 5 HC: 6.8
+NP_001121846.1 scaffold_1 8.33 91 24 9 1 27 17 107 5.5 0 0.0 6.64 0.58 7 3 0 0 .
+NP_001121846.1 scaffold_1 65.85 122 14 0 28 68 418 539 21.2 310 -1.7 1.88 0.83 6 2 0 1 GT.AG
+NP_001121846.1 scaffold_1 64.29 127 15 0 69 110 7124 7250 18.9 6584 -3.1 1.77 1.71 4 0 0 0 GT.AG
+NP_001121846.1 scaffold_1 19.05 147 30 21 111 152 44187 44333 3.0 36936 -4.2 1.03 1.02 6 1 0 1 GT.AG
+NP_001121846.1 scaffold_1 15.00 224 52 30 153 222 44595 44818 -3.3 261 -1.6 1.50 0.00 8 0 0 1 GT.AG
+@ scaffold_1 + ( 17 44818 ) NP_001121846.1 [1:222] ( 1 222 ) S: 243.6 =: 37.8 C: 98.6 T#: 135 T-: 60 B#: 24 B-: 9 X: 0 Nexn: 5 HC: 6.8