# HG changeset patch
# User iuc
# Date 1760544166 0
# Node ID 31df46f4274e18474b581483c142960d70e7ec44
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
diff -r 000000000000 -r 31df46f4274e cawlign.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cawlign.xml Wed Oct 15 16:02:46 2025 +0000
@@ -0,0 +1,264 @@
+
+ Codon-aware (pairwise) alignment
+
+ macros.xml
+
+
+
+ '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ OQ948666.1-indel
+ CCTCAAATCACTCTTTGGCAGCGACCCATTGTCACAATAAGGGTAGGGGGGCAATTAAAG...
+
+ **refalign**
+
+ The `refalign` output format also aligns the query sequences to the reference but *does* retain insertions, which are shown in lowercase.
+
+ .. code-block:: text
+
+ >OQ948666.1-indel
+ CCTCAAATCACTCTTTGGCAGCGACCCATTGTCACgatacaAATAAGGGTAGGGGGGCAATTAAAG...
+
+ **pairwise**
+
+ The `pairwise` output format reports the full pairwise alignment, including the reference sequence, with insertions and deletions shown as gaps in the corresponding sequence.
+
+ .. code-block:: text
+
+ >HXB2_pol
+ CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCAC------AATAAAGATAGGGGGGCAACTAAAG...
+ >OQ948666.1-indel
+ CCTCAAATCACTCTTTGGCAGCGACCCATTGTCACGATACAAATAAGGGTAGGGGGGCAATTAAAG...
+
+ .. class:: infomalign
+
+ **References**
+
+ For more information, please visit the `cawlign` GitHub repository: https://github.com/veg/cawlign
+ ]]>
+
+
\ No newline at end of file
diff -r 000000000000 -r 31df46f4274e macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Oct 15 16:02:46 2025 +0000
@@ -0,0 +1,26 @@
+
+ 0.1.14
+ 0
+
+
+ cawlign
+
+
+
+
+
+
+
+
+
+ @misc{githubcawlign,
+ author = {Pond, Sergei and Weaver, Steven and Moshiri, Niema and Hepler, Lance},
+ year = {2025},
+ title = {cawlign: a C++ port of bealign},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/veg/cawlign}
+ }
+
+
+
diff -r 000000000000 -r 31df46f4274e test-data/OQ948666-pr-int-indel.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OQ948666-pr-int-indel.fa Wed Oct 15 16:02:46 2025 +0000
@@ -0,0 +1,2 @@
+>OQ948666.1-indel
+CCTCAAATCACTCTTTGGCAGCGACCCATTGTCACgatacaAATAAGGGTAGGGGGGCAATTAAAGGAAGCCCTATTAGATACAGGAGCAGATGATACAGTGTTAGAAGAAATGGATTTGCCAGGAAGATGGAAGCCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAGCAGATAACCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTAACTCAGCTTGGTTGCACTTTAAATTTTATGTAGATGGGGCAGCCAACAGGGAGACTAAATTGGGAAAAGCAGGATATGTTACTAACAGAGGAAGACAAAGGGTTGTCACCTTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTCATCTAGCTTTGCAGGATTCAGGATCAGAAGTAAACATAGTAACAGACTCACAGTATGCACTTGGAATCATCCAAGCACACCCAGATAGAAGTGAATCAGGGATAGTCAATCAAATCATAGAGCAGCTAATAAAAAAGGAAAAGGTCTACCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTTAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGAAAAGGCACAGGAAGAACATGAGAAATATCACAATAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCAGCTGTAGTAGCAAAAGAAATAGTAGCCTGCTGTGATAAATGCCAGATAAAGGGAGAAGCTATACATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTTCAGCAGAGACAGGGCAGGAAACAGCCTACTTCATCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACAGACAATGGCAGCAATTTCACCAGTGCTACAGTTAAGGCCGCCTGTTGGTGGGCAGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAATGCATTAAAGAAAATTATAGGACAGGTAAGAGAGCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCATCAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAACTTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAGACCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATCAGGACATAAAAGTAGTGCCAAGAAGGAAAGCAAAGATTATCAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAGGTAGACAGGATGAGGA
diff -r 000000000000 -r 31df46f4274e test-data/expected-result.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected-result.fa Wed Oct 15 16:02:46 2025 +0000
@@ -0,0 +1,2 @@
+>OQ948666.1-indel
+CCTCAAATCACTCTTTGGCAGCGACCCATTGTCACGATACAAATAagggtaGGGGGGCAATTAAAGGAAGCCCTATTAGATACAGGAGCAGATGATACAGTGTTAGAAGAAATGGATTTGCCAGGAAGATGGAAGCCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAGCAGATAACCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTAACTCAGCTTGGTTGCACTTTAAA-TTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATGTAGATGGGGCAGCCAACAGGGAGACTAAATTGGGAAAAGCAGGATATGTTACTAACAGAGGAAGACAAAGGGTTGTCACCTTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTCATCTAGCTTTGCAGGATTCAGGATCAGAAGTAAACATAGTAACAGACTCACAGTATGCACTTGGAATCATCCAAGCACACCCAGATAGAAGTGAATCAGGGATAGTCAATCAAATCATAGAGCAGCTAATAAAAAAGGAAAAGGTCTACCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTTAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGAAAAGGCACAGGAAGAACATGAGAAATATCACAATAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCAGCTGTAGTAGCAAAAGAAATAGTAGCCTGCTGTGATAAATGCCAGATAAAGGGAGAAGCTATACATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTTCAGCAGAGACAGGGCAGGAAACAGCCTACTTCATCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACAGACAATGGCAGCAATTTCACCAGTGCTACAGTTAAGGCCGCCTGTTGGTGGGCAGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAATGCATTAAAGAAAATTATAGGACAGGTAAGAGAGCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCATCAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAACTTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAGACCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATCAGGACATAAAAGTAGTGCCAAGAAGGAAAGCAAAGATTATCAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAGGTAGACAGGATGAGGA-