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a95ae512
Commit
a95ae512
authored
Oct 27, 2015
by
Eric Coissac
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Change the ecotag doc according to the new -M option
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0e2f8598
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ecotag.rst
doc/sphinx/source/scripts/ecotag.rst
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doc/sphinx/source/scripts/ecotag.rst
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a95ae512
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@@ -15,7 +15,7 @@
output file. FLOAT is included in a [0,1] interval.
.. cmdoption:: --minimum-circle=FLOAT
minimum identity considered for the assignment circle.
FLOAT is included in a [0,1] interval.
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@@ -40,11 +40,20 @@
.. cmdoption:: -E FLOAT, --errors=FLOAT
FLOAT is the fraction of reference sequences that will
be ignored when looking for the
most recen
t common ancestor. This
be ignored when looking for the
lowes
t common ancestor. This
option is useful when a non-negligible proportion of reference sequences
is expected to be assigned to the wrong taxon, for example because of
taxonomic misidentification. FLOAT is included in a [0,1] interval.
.. cmdoption:: -M INTEGER, --min-matches=FLOAT
Define the minimum congruent assignation. If this minimum is reached and
the -E option is activated, the lowest common ancestor algorithm tolarated
that some sequences do not provide the same taxonomic annotation (see the
-E option).
.. cmdoption:: --cache-size=INTEGER
A cache for computed similarities is maintained by `ecotag`. the default
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