annotate mothur/tool-data/mothur_calulators.loc @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

#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):
# 
# venn	sobs,chao,ace	sharedsobs,sharedchao,sharedace
# rarefaction.shared	sharednseqs,sharedobserved
# rarefaction.single	ace,bootstrap,chao,coverage,heip,invsimpson,jack,npshannon,nseqs,shannon,shannoneven,simpson,simpsoneven,smithwilson,sobs
# dist.shared	braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc
# tree.shared	braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc
# heatmap.sim	braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc
# collect.shared	anderberg,braycurtis,jabund,jclass,jest,kstest,kulczynski,kulczynskicody,lennon,morisitahorn,ochiai,sharedace,sharedchao,sharednseqs,sharedsobs,sorabund,sorclass,sorest,thetan,thetayc,whittaker
# summary.shared	anderberg,braycurtis,jabund,jclass,jest,kstest,kulczynski,kulczynskicody,lennon,morisitahorn,ochiai,sharedace,sharedchao,sharednseqs,sharedsobs,sorabund,sorclass,sorest,thetan,thetayc,whittaker
# collect.single	ace,bergerparker,boneh,bootstrap,bstick,chao,coverage,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,efron,geometric,goodscoverage,heip,invsimpson,jack,logseries,npshannon,nseqs,qstat,shannon,shannoneven,shen,simpson,simpsoneven,smithwilson,sobs,solow
#
#<calculator>	<mult>	<mult2>	<category>	<description>
#
#Community richness	
sobs	single	sing	Community richness	the observed richness
chao	single	sing	Community richness	the Chao1 estimator
ace	single	sing	Community richness	the ACE estimator
jack	single	sing	Community richness	the jackknife estimator
bootstrap	single	sing	Community richness	the bootstrap estimator
#Community diversity
bergerparker	single	xxxx	Community diversity	the Berger-Parker index
shannon	single	sing	Community diversity	the Shannon index
npshannon	single	sing	Community diversity	the non-parametric Shannon index
simpson	single	sing	Community diversity	the Simpson index
simpsoneven	single	sing	Community diversity	the Simpson index
invsimpson	single	sing	Community diversity	the Simpson index
coverage	single	sing	Community diversity	the sampling coverage coverage
qstat	single	xxxx	Community diversity	the Q statistic
#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
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
#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
#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