annotate mothur/tool-data/mothur_calculators.loc @ 8:3249eb52a9c1

trim.seqs name parameter needs to be optional

#This is a sample file distributed with Galaxy that enables 
# Mothur tools to present a choice of values for calculators
# source -  http://www.mothur.org/wiki/Calculators
#file has this format (fields are separated by TAB characters):
# 
##
# collect.single	ace, bergerparker, boneh, bootstrap, bstick, chao, coverage, default, efron, geometric, goodscoverage, heip, invsimpson, jack, logseries, npshannon, nseqs, qstat, shannon, shannoneven, shen, simpson, simpsoneven, smithwilson, sobs, solow
# summary.single	ace, bergerparker, boneh, bootstrap, bstick, chao, coverage, default, efron, geometric, goodscoverage, heip, invsimpson, jack, logseries, npshannon, nseqs, qstat, shannon, shannoneven, shen, simpson, simpsoneven, smithwilson, sobs, solow
# rarefaction.single	ace,                      bootstrap,         chao, coverage, default,                                  heip, invsimpson, jack,            npshannon, nseqs,        shannon, shannoneven,       simpson, simpsoneven, smithwilson, sobs
##
# collect.shared	anderberg, braycurtis, canberra, default, gower, hamming, hellinger, jabund, jclass, jest, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker
# summary.shared	anderberg, braycurtis, canberra, default, gower, hamming, hellinger, jabund, jclass, jest, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker
# dist.shared		anderberg, braycurtis, canberra,          gower, hamming, hellinger, jabund, jclass, jest, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker
# tree.shared		anderberg, braycurtis, canberra,          gower, hamming, hellinger, jabund, jclass, jest, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker
# heatmap.sim		           braycurtis,                                               jabund, jclass, jest,                                                                                                     morisitahorn,                                                                        sorabund, sorclass, sorest,                                                                                                      thetan, thetayc
##
# venn	sobs,chao,ace	sharedsobs,sharedchao,sharedace
# rarefaction.shared	sharednseqs,sharedobserved
#
##
#<calculator>	<mult>	<mult2>	<category>	<description>
#
##Community richness	
ace	single	sing	Community richness	the ACE estimator
bootstrap	single	sing	Community richness	the bootstrap estimator
chao	single	sing	Community richness	the Chao1 estimator
jack	single	sing	Community richness	the jackknife estimator
sobs	single	sing	Community richness	the observed richness
##Community evenness
simpsoneven	single	sing	Community evenness	a Simpson index-based measure of evenness
shannoneven	single	sing	Community evenness	a Shannon index-based measure of evenness
heip	single	sing	Community evenness	Heip's metric of community evenness
smithwilson	single	sing	Community evenness	Smith and Wilson's metric of community evenness
##Community diversity
bergerparker	single	xxxx	Community diversity	the Berger-Parker index
coverage	single	sing	Community diversity	the sampling coverage 
goodscoverage	single	sing	Community diversity	the Good's estimate of sampling coverage 
invsimpson	single	sing	Community diversity	the Simpson index
npshannon	single	sing	Community diversity	the non-parametric Shannon index
qstat	single	xxxx	Community diversity	the Q statistic
shannon	single	sing	Community diversity	the Shannon index
simpson	single	sing	Community diversity	the Simpson index
##Estimates of number of additional OTUs observed with extra sampling
boneh	single	xxxx	Estimator	Boneh's estimator
efron	single	xxxx	Estimator	Efron's estimator
shen	single	xxxx	Estimator	Shen's estimator
solow	single	xxxx	Estimator	Solow's estimator
##Statistical distributions
logseries	single	xxxx	Statistical distribution	tests whether observed data follow the log series distribution
geometric	single	xxxx	Statistical distribution	tests whether observed data follow the geometric series distribution
bstick	single	xxxx	Statistical distribution	tests whether observed data follow the broken stick distribution
## Shared community richness
sharedsobs	shared	xxxx	Shared community richness	the observed richness shared between two or more samples
sharedchao	shared	xxxx	Shared community richness	the two or more sample shared Chao1 richness estimator
sharedace	shared	xxxx	Shared community richness	the two sample shared ACE richness estimator
##Similarity in community membership
anderberg	shared	xxxx	Community Membership Similarity	the Anderberg similarity coefficient
jclass	shared	shar	Community Membership Similarity	the traditional Jaccard similarity coefficient based on the observed richness
jest	shared	shar	Community Membership Similarity	the Jaccard similarity coefficient based on the Chao1 estimated richnesses
kulczynski	shared	xxxx	Community Membership Similarity	the Kulczynski similarity coefficient
kulczynskicody	shared	xxxx	Community Membership Similarity	the Kulczynski-Cody similarity coefficient
kstest	shared	xxxx	Kolmogorov-Smirnov test 
lennon	shared	xxxx	Community Membership Similarity	the Lennon similarity coefficient
ochiai	shared	xxxx	Community Membership Similarity	the Ochiai similarity coefficient
sorclass	shared	shar	Community Membership Similarity	the Sorenson similarity coefficient based on the observed richness
sorest	shared	shar	Community Membership Similarity	the Sorenson similarity coefficient based on the Chao1 estimated richnesses
whittaker	shared	xxxx	Community Membership Similarity	the Whittaker similarity coefficient
hamming	shared	xxxx	Community Membership Similarity	-
memchi2	shared	xxxx	Community Membership Similarity	-
memchord	shared	xxxx	Community Membership Similarity	-
memeuclidean	shared	xxxx	Community Membership Similarity	-
mempearson	shared	xxxx	Community Membership Similarity	-
##Similarity in community structure
braycurtis	shared	shar	Community Structure Similarity	the Bray-Curtis similarity coefficient
jabund	shared	shar	Community Structure Similarity	the abundance-based Jaccard similarity coefficient
morisitahorn	shared	shar	Community Structure Similarity	the Morisita-Horn similarity coefficient
sorabund	shared	shar	Community Structure Similarity	the abundance-based Sorenson similarity coefficient
thetan	shared	shar	Community Structure Similarity	the Smith theta similarity coefficient
thetayc	shared	shar	Community Structure Similarity	the Yue & Clayton theta similarity coefficient
canberra	shared	xxxx	Community Structure Similarity	-
gower	shared	xxxx	Community Structure Similarity	-
hellinger	shared	xxxx	Community Structure Similarity	-
manhattan	shared	xxxx	Community Structure Similarity	-
odum	shared	xxxx	Community Structure Similarity	-
soergel	shared	xxxx	Community Structure Similarity	-
spearman	shared	xxxx	Community Structure Similarity	-
speciesprofile	shared	xxxx	Community Structure Similarity	-
structchi2	shared	xxxx	Community Structure Similarity	-
structchord	shared	xxxx	Community Structure Similarity	-
structeuclidean	shared	xxxx	Community Structure Similarity	-
structkulczynski	shared	xxxx	Community Structure Similarity	-
structpearson	shared	xxxx	Community Structure Similarity	-
##Utility calculators
nseqs	single	sing	Utility	the number of sequences in a sample
sharednseqs	shared	rare	Utility	the number of sequences in two samples
sharedobserved	shared	rare	Utility	the number of sequences in two samples