# HG changeset patch
# User nml
# Date 1467899937 14400
# Node ID b81f1de20067b57aaba83115fd701bbd4cc95720
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
diff -r 000000000000 -r b81f1de20067 hivtrace.xml
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+++ b/hivtrace.xml Thu Jul 07 09:58:57 2016 -0400
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+ with options and commands
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+ hivtrace
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+ $outfile
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+ The sequence that will be used to align everything else to.
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+ How to handle analyses of proteins (HIV-1 pr and/or RT only) which include drug resistance associated positions
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+ How to handle analyses of proteins (HIV-1 pr and/or RT only) which include drug resistance associated positions
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+ How to handle analyses of proteins (HIV-1 pr and/or RT only) which include drug resistance associated positions
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+ How to handle analyses of proteins (HIV-1 pr and/or RT only) which include drug resistance associated positions
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+ What should be done if query sequences belong to the same cluster as the reference. If the reference is a database/lab strain (e.g. HXB2),
+ such sequences are likely mislabeled/contaminated.
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+ Use a phylogenetic test of conditional independence on each triangle in the network to remove spurious transitive connections which make A→B→C chains look like A-B-C triangles.
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+ Procedure for handling IUPAC ambiguities
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+ B->C chains look like A-B-C triangles
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+-----
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+**Handle ambiguities**
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+Handle ambiguious nucleotides using one of the following specified strategies.
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+*Resolve* - count any resolutions that match as a perfect match
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+*Average* - average all possible resolutions
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+*Skip* - skip all positions with ambiguities
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+*GAPMM* - count character-gap positions as 4-way mismatches, otherwise same as average
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+For more details, please see the the MBE paper: http://mbe.oxfordjournals.org/content/22/5/1208.short
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+-----
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+**Ambiguity fraction**
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+.. class:: infomark
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+**TIP:** This option is only available when *Handle ambiguities* is set to Resolve
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+Affects only the Resolve option for handling ambiguities. Any sequence with no more than the selected proportion [0 - 1] will have its ambiguities resolved (if possible), and ambiguities in sequences with higher fractions of them will be averaged. This mitigates spurious linkages due to highly ambiguous sequences
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+**Compare to Los Alamos National Laboratory HIV database sequences**
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+.. class:: infomark
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+**TIP:** This option is only available for specific reference types
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+Compare uploaded sequences to all public sequences. Retrieved periodically from the Los Alamos HIV Sequence Database: http://hiv.lanl.gov/
+ ]]>
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diff -r 000000000000 -r b81f1de20067 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Jul 07 09:58:57 2016 -0400
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