Mercurial > repos > iuc > ucsc_axtchain

comparison axtchain.xml @ 2:05afdd33dac7 draft default tip

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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
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1:54a6fb045aea 2:05afdd33dac7
70 <help><![CDATA[ 70 <help><![CDATA[
71 **What it does** 71 **What it does**
72 72
73 `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. 73 `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.
74 74
75 For implementation details see axtChain's `source code`_.
75 76
76 sample linearGap file (loose):: 77 linearGap defaults:
77 78
78 tablesize 11 79 loose::
79 smallSize 111
80 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
81 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
82 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
83 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
84 80
85 For implementation details see axtChain's `source code`_. 81 tablesize 11
82 smallSize 111
83 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
84 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
85 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
86 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
87
88 medium::
89
90 tableSize 11
91 smallSize 111
92 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
93 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
94 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
95 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300
96
86 97
87 .. _axtChain: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt 98 .. _axtChain: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
88 .. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html 99 .. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
89 .. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html 100 .. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
90 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/axtChain/axtChain.c 101 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/axtChain/axtChain.c