Mercurial > repos > iuc > ucsc_axtchain
diff axtchain.xml @ 2:05afdd33dac7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
| author | iuc |
|---|---|
| date | Thu, 26 Sep 2024 16:52:30 +0000 |
| parents | 54a6fb045aea |
| children |
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--- a/axtchain.xml Sun Sep 22 07:26:47 2024 +0000 +++ b/axtchain.xml Thu Sep 26 16:52:30 2024 +0000 @@ -72,17 +72,28 @@ `axtChain`_ is a tool to chain together alignments in `axt`_ format. The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously. +For implementation details see axtChain's `source code`_. -sample linearGap file (loose):: +linearGap defaults: + +loose:: - tablesize 11 - smallSize 111 - position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 - qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 - tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 - bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 + tablesize 11 + smallSize 111 + position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 + qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 + tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 + bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 -For implementation details see axtChain's `source code`_. +medium:: + + tableSize 11 + smallSize 111 + position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 + qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 + tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 + bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 + .. _axtChain: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt .. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html