# HG changeset patch
# User iuc
# Date 1682194120 0
# Node ID 7adddc6015c1dd0dc6743364dbaef092ff5973c3
# Parent  1080e07a22333b22602e3b9eb053542a97e35092
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit a59b05dd4a79b1b4e14ab1d78202c07a889ab023

diff -r 1080e07a2233 -r 7adddc6015c1 test-data/interval2maf-out1.maf
--- a/test-data/interval2maf-out1.maf	Wed Nov 09 12:34:55 2022 +0000
+++ b/test-data/interval2maf-out1.maf	Sat Apr 22 20:08:40 2023 +0000
@@ -666,7 +666,9 @@
 a score=6521322.0
 s hg38.chr22             21635217 49 + 50818468 CTCCCCCTCCATGTCTAGTGC---CCAGGTGGCCACCAGATTCAAACTCAAG 
 s eulFla1.LGHW01001899v1   119076 49 +   262521 CTCCCCCTCCACGTCTAATGC---CCAGATCGCCACCAAATTCAGGCTCAAG 
+i eulFla1.LGHW01001899v1                        I 1 C 0                                              
 s mm10.chr16             81066123 46 - 98207768 ------CTCCCCACCTAATGCAGTCCAGATGGCTACCAGATTCAGGCTCAAG 
+i mm10.chr16                                    C 0 C 0                                              
 
 a score=31953654.0
 s hg38.chr22             21634684 360 + 50818468 AAAGGCCTCAGTCAGTCCTGCTCCCAGAGGGACTCCCTGCTGTGGGATTCGCTGGGTAGCCAGACCAGCTTTCAGTGGACACAGGAGCAGCCCTTGTCCTGGTTCTCAGGGCTGCTGGGCTCAAGCTCTGGCGTGCCTGAAGCATCAGAGCCGAGGCCTGGAGAACAGGAGCCAATCTTCCGCAAGCGAGAGTTCAATAAGGAGATCAAGTCATTACTGAGCCAGCTGGAGTCCCTCGACCTGCCTGGCTACTGTCCGCTCCGTGAGCCCCATCGCACGCTGAACTTCCTGGCTGACCACCGCCTCTTCCCTGCCCTGCAAAGCGTGGTCAGCCAGGCTGTGGATAAGCTCCGTGGCGCC 
@@ -933,6 +935,7 @@
 a score=5438213.0
 s hg38.chr22 23394222 60 + 50818468 ATGGCGAGCATGGCAGTGAGCCCCCCACGCCCCACTCTGGGTCTGGAGACCAGCCCCCCA 
 s mm10.chr16 18219555 48 + 98207768 ATG------ATGGAGGTAAGTCCCC---ACCCCATTCCTGCT---GATTCCAGCGTCCCC 
+i mm10.chr16                        C 0 C 0                                                      
 
 a score=5438213.0
 s hg38.chr22 23394222 60 + 50818468 ATGGCGAGCATGGCAGTGAGCCCCCCACGCCCCACTCTGGGTCTGGAGACCAGCCCCCCA 
@@ -2346,6 +2349,7 @@
 a score=799075.0
 s hg38.chr22             35726271 16 + 50818468 TGATGAGGCTGGTATG 
 s eulFla1.LGHW01001967v1   331202 16 +   548553 TGAAGAGGCTAGCGTG 
+i eulFla1.LGHW01001967v1                        C 0 C 0          
 
 a score=799075.0
 s hg38.chr22             35726271 16 + 50818468 TGATGAGGCTGGTATG 
@@ -2595,12 +2599,14 @@
 s hg38.chr22 35727139 55 + 50818468 TGTTCCAGCTCCCGGGGCAGGGCTGTTCGAGGATCCCGTGTGGTTAAACCAGAAG 
 
 a score=799075.0
-s hg38.chr22             35726284 3 + 50818468 ATG 
-s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG 
+s hg38.chr22             35726284 3 + 50818468 ATG     
+s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG     
+i eulFla1.LGHW01001967v1                       C 0 C 0 
 
 a score=799075.0
-s hg38.chr22             35726284 3 + 50818468 ATG 
-s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG 
+s hg38.chr22             35726284 3 + 50818468 ATG     
+s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG     
+i eulFla1.LGHW01001967v1                       C 0 C 0 
 
 a score=799075.0
 s hg38.chr22             35726284 3 + 50818468 ATG     
diff -r 1080e07a2233 -r 7adddc6015c1 test-data/interval2maf-out2.maf
--- a/test-data/interval2maf-out2.maf	Wed Nov 09 12:34:55 2022 +0000
+++ b/test-data/interval2maf-out2.maf	Sat Apr 22 20:08:40 2023 +0000
@@ -344,7 +344,9 @@
 a score=6521322.0
 s hg38.chr22             21635217 49 + 50818468 CTCCCCCTCCATGTCTAGTGC---CCAGGTGGCCACCAGATTCAAACTCAAG 
 s eulFla1.LGHW01001899v1   119076 49 +   262521 CTCCCCCTCCACGTCTAATGC---CCAGATCGCCACCAAATTCAGGCTCAAG 
+i eulFla1.LGHW01001899v1                        I 1 C 0                                              
 s mm10.chr16             81066123 46 - 98207768 ------CTCCCCACCTAATGCAGTCCAGATGGCTACCAGATTCAGGCTCAAG 
+i mm10.chr16                                    C 0 C 0                                              
 
 a score=31953654.0
 s hg38.chr22             21634684 360 + 50818468 AAAGGCCTCAGTCAGTCCTGCTCCCAGAGGGACTCCCTGCTGTGGGATTCGCTGGGTAGCCAGACCAGCTTTCAGTGGACACAGGAGCAGCCCTTGTCCTGGTTCTCAGGGCTGCTGGGCTCAAGCTCTGGCGTGCCTGAAGCATCAGAGCCGAGGCCTGGAGAACAGGAGCCAATCTTCCGCAAGCGAGAGTTCAATAAGGAGATCAAGTCATTACTGAGCCAGCTGGAGTCCCTCGACCTGCCTGGCTACTGTCCGCTCCGTGAGCCCCATCGCACGCTGAACTTCCTGGCTGACCACCGCCTCTTCCCTGCCCTGCAAAGCGTGGTCAGCCAGGCTGTGGATAAGCTCCGTGGCGCC 
@@ -611,6 +613,7 @@
 a score=5438213.0
 s hg38.chr22 23394222 60 + 50818468 ATGGCGAGCATGGCAGTGAGCCCCCCACGCCCCACTCTGGGTCTGGAGACCAGCCCCCCA 
 s mm10.chr16 18219555 48 + 98207768 ATG------ATGGAGGTAAGTCCCC---ACCCCATTCCTGCT---GATTCCAGCGTCCCC 
+i mm10.chr16                        C 0 C 0                                                      
 
 a score=5438213.0
 s hg38.chr22 23394222 60 + 50818468 ATGGCGAGCATGGCAGTGAGCCCCCCACGCCCCACTCTGGGTCTGGAGACCAGCCCCCCA 
@@ -2221,6 +2224,7 @@
 a score=799075.0
 s hg38.chr22             35726271 16 + 50818468 TGATGAGGCTGGTATG 
 s eulFla1.LGHW01001967v1   331202 16 +   548553 TGAAGAGGCTAGCGTG 
+i eulFla1.LGHW01001967v1                        C 0 C 0          
 
 a score=201690.0
 s hg38.chr22             35726287 11 + 50818468 CTGTCCTACTT 
@@ -2304,6 +2308,7 @@
 a score=799075.0
 s hg38.chr22             35726271 16 + 50818468 TGATGAGGCTGGTATG 
 s eulFla1.LGHW01001967v1   331202 16 +   548553 TGAAGAGGCTAGCGTG 
+i eulFla1.LGHW01001967v1                        C 0 C 0          
 
 a score=799075.0
 s hg38.chr22             35726271 16 + 50818468 TGATGAGGCTGGTATG 
@@ -2553,8 +2558,9 @@
 s hg38.chr22 35727139 55 + 50818468 TGTTCCAGCTCCCGGGGCAGGGCTGTTCGAGGATCCCGTGTGGTTAAACCAGAAG 
 
 a score=799075.0
-s hg38.chr22             35726284 3 + 50818468 ATG 
-s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG 
+s hg38.chr22             35726284 3 + 50818468 ATG     
+s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG     
+i eulFla1.LGHW01001967v1                       C 0 C 0 
 
 a score=201690.0
 s hg38.chr22             35726287 11 + 50818468 CTGTCCTACTT 
@@ -2636,12 +2642,14 @@
 s hg38.chr22 35727139 55 + 50818468 TGTTCCAGCTCCCGGGGCAGGGCTGTTCGAGGATCCCGTGTGGTTAAACCAGAAG 
 
 a score=799075.0
-s hg38.chr22             35726284 3 + 50818468 ATG 
-s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG 
+s hg38.chr22             35726284 3 + 50818468 ATG     
+s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG     
+i eulFla1.LGHW01001967v1                       C 0 C 0 
 
 a score=799075.0
-s hg38.chr22             35726284 3 + 50818468 ATG 
-s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG 
+s hg38.chr22             35726284 3 + 50818468 ATG     
+s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG     
+i eulFla1.LGHW01001967v1                       C 0 C 0 
 
 a score=799075.0
 s hg38.chr22             35726284 3 + 50818468 ATG     
diff -r 1080e07a2233 -r 7adddc6015c1 test-data/interval2maf-out3.maf
--- a/test-data/interval2maf-out3.maf	Wed Nov 09 12:34:55 2022 +0000
+++ b/test-data/interval2maf-out3.maf	Sat Apr 22 20:08:40 2023 +0000
@@ -344,7 +344,9 @@
 a score=6521322.0
 s hg38.chr22             21635217 49 + 50818468 CTCCCCCTCCATGTCTAGTGC---CCAGGTGGCCACCAGATTCAAACTCAAG 
 s eulFla1.LGHW01001899v1   119076 49 +   262521 CTCCCCCTCCACGTCTAATGC---CCAGATCGCCACCAAATTCAGGCTCAAG 
+i eulFla1.LGHW01001899v1                        I 1 C 0                                              
 s mm10.chr16             81066123 46 - 98207768 ------CTCCCCACCTAATGCAGTCCAGATGGCTACCAGATTCAGGCTCAAG 
+i mm10.chr16                                    C 0 C 0                                              
 
 a score=31953654.0
 s hg38.chr22             21634684 360 + 50818468 AAAGGCCTCAGTCAGTCCTGCTCCCAGAGGGACTCCCTGCTGTGGGATTCGCTGGGTAGCCAGACCAGCTTTCAGTGGACACAGGAGCAGCCCTTGTCCTGGTTCTCAGGGCTGCTGGGCTCAAGCTCTGGCGTGCCTGAAGCATCAGAGCCGAGGCCTGGAGAACAGGAGCCAATCTTCCGCAAGCGAGAGTTCAATAAGGAGATCAAGTCATTACTGAGCCAGCTGGAGTCCCTCGACCTGCCTGGCTACTGTCCGCTCCGTGAGCCCCATCGCACGCTGAACTTCCTGGCTGACCACCGCCTCTTCCCTGCCCTGCAAAGCGTGGTCAGCCAGGCTGTGGATAAGCTCCGTGGCGCC 
@@ -611,6 +613,7 @@
 a score=5438213.0
 s hg38.chr22 23394222 60 + 50818468 ATGGCGAGCATGGCAGTGAGCCCCCCACGCCCCACTCTGGGTCTGGAGACCAGCCCCCCA 
 s mm10.chr16 18219555 48 + 98207768 ATG------ATGGAGGTAAGTCCCC---ACCCCATTCCTGCT---GATTCCAGCGTCCCC 
+i mm10.chr16                        C 0 C 0                                                      
 
 a score=5438213.0
 s hg38.chr22 23394222 60 + 50818468 ATGGCGAGCATGGCAGTGAGCCCCCCACGCCCCACTCTGGGTCTGGAGACCAGCCCCCCA 
@@ -2221,6 +2224,7 @@
 a score=799075.0
 s hg38.chr22             35726271 16 + 50818468 TGATGAGGCTGGTATG 
 s eulFla1.LGHW01001967v1   331202 16 +   548553 TGAAGAGGCTAGCGTG 
+i eulFla1.LGHW01001967v1                        C 0 C 0          
 
 a score=201690.0
 s hg38.chr22             35726287 11 + 50818468 CTGTCCTACTT 
@@ -2304,6 +2308,7 @@
 a score=799075.0
 s hg38.chr22             35726271 16 + 50818468 TGATGAGGCTGGTATG 
 s eulFla1.LGHW01001967v1   331202 16 +   548553 TGAAGAGGCTAGCGTG 
+i eulFla1.LGHW01001967v1                        C 0 C 0          
 
 a score=799075.0
 s hg38.chr22             35726271 16 + 50818468 TGATGAGGCTGGTATG 
@@ -2553,8 +2558,9 @@
 s hg38.chr22 35727139 55 + 50818468 TGTTCCAGCTCCCGGGGCAGGGCTGTTCGAGGATCCCGTGTGGTTAAACCAGAAG 
 
 a score=799075.0
-s hg38.chr22             35726284 3 + 50818468 ATG 
-s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG 
+s hg38.chr22             35726284 3 + 50818468 ATG     
+s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG     
+i eulFla1.LGHW01001967v1                       C 0 C 0 
 
 a score=201690.0
 s hg38.chr22             35726287 11 + 50818468 CTGTCCTACTT 
@@ -2636,12 +2642,14 @@
 s hg38.chr22 35727139 55 + 50818468 TGTTCCAGCTCCCGGGGCAGGGCTGTTCGAGGATCCCGTGTGGTTAAACCAGAAG 
 
 a score=799075.0
-s hg38.chr22             35726284 3 + 50818468 ATG 
-s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG 
+s hg38.chr22             35726284 3 + 50818468 ATG     
+s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG     
+i eulFla1.LGHW01001967v1                       C 0 C 0 
 
 a score=799075.0
-s hg38.chr22             35726284 3 + 50818468 ATG 
-s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG 
+s hg38.chr22             35726284 3 + 50818468 ATG     
+s eulFla1.LGHW01001967v1   331215 3 +   548553 GTG     
+i eulFla1.LGHW01001967v1                       C 0 C 0 
 
 a score=799075.0
 s hg38.chr22             35726284 3 + 50818468 ATG