# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1326831404 21600
# Node ID d869876010224858d59a55edf14949a54a704717
# Parent  6971568061623df4f4fbe163eaca6442f832a5d2
Move calc options in individual tools and remove tool-data/mothur_calculators.loc

diff -r 697156806162 -r d86987601022 mothur/tool-data/mothur_calculators.loc
--- a/mothur/tool-data/mothur_calculators.loc	Tue Jan 17 11:22:44 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,98 +0,0 @@
-#This is a sample file distributed with Galaxy that enables 
-# Mothur tools to present a choice of values for calculators
-#   (There aren't any local files to point to, so this doesn't need to be modified)
-# 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
diff -r 697156806162 -r d86987601022 mothur/tool-data/mothur_calculators.loc.sample
--- a/mothur/tool-data/mothur_calculators.loc.sample	Tue Jan 17 11:22:44 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,98 +0,0 @@
-#This is a sample file distributed with Galaxy that enables 
-# Mothur tools to present a choice of values for calculators
-#   (There aren't any local files to point to, so this doesn't need to be modified)
-# 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
diff -r 697156806162 -r d86987601022 mothur/tools/mothur/collect.shared.xml
--- a/mothur/tools/mothur/collect.shared.xml	Tue Jan 17 11:22:44 2012 -0600
+++ b/mothur/tools/mothur/collect.shared.xml	Tue Jan 17 14:16:44 2012 -0600
@@ -43,15 +43,48 @@
    </options>
   </param>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none are selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult" index="1"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult" column="1" value="shared" />
-   </options>
+   <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
+   <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
+   <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
+   <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
+   <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
+   <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
+   <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
+   <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
+   <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
+   <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
+   <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
+   <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
+   <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
+   <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
+   <option value="hamming">hamming - Community Membership Similarity -</option>
+   <option value="memchi2">memchi2 - Community Membership Similarity -</option>
+   <option value="memchord">memchord - Community Membership Similarity -</option>
+   <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
+   <option value="mempearson">mempearson - Community Membership Similarity -</option>
+   <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
+   <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
+   <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
+   <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
+   <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
+   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option>
+   <option value="canberra">canberra - Community Structure Similarity -</option>
+   <option value="gower">gower - Community Structure Similarity -</option>
+   <option value="hellinger">hellinger - Community Structure Similarity -</option>
+   <option value="manhattan">manhattan - Community Structure Similarity -</option>
+   <option value="odum">odum - Community Structure Similarity -</option>
+   <option value="soergel">soergel - Community Structure Similarity -</option>
+   <option value="spearman">spearman - Community Structure Similarity -</option>
+   <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
+   <option value="structchi2">structchi2 - Community Structure Similarity -</option>
+   <option value="structchord">structchord - Community Structure Similarity -</option>
+   <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
+   <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
+   <option value="structpearson">structpearson - Community Structure Similarity -</option>
+   <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
+   <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
   </param>
   <param name="freq" type="float" value="0.0" label="freq - "/>
-
   <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
  </inputs>
  <outputs>
diff -r 697156806162 -r d86987601022 mothur/tools/mothur/collect.single.xml
--- a/mothur/tools/mothur/collect.single.xml	Tue Jan 17 11:22:44 2012 -0600
+++ b/mothur/tools/mothur/collect.single.xml	Tue Jan 17 14:16:44 2012 -0600
@@ -44,12 +44,31 @@
    </options>
   </param>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult" index="1"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult" column="1" value="single" />
-   </options>
+   <option value="ace" selected="true">ace - Community richness the ACE estimator</option>
+   <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
+   <option value="chao" selected="true">chao - Community richness the Chao1 estimator</option>
+   <option value="jack" selected="true">jack - Community richness the jackknife estimator</option>
+   <option value="sobs" selected="true">sobs - Community richness the observed richness</option>
+   <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option>
+   <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option>
+   <option value="heip">heip - Community evenness Heip's metric of community evenness</option>
+   <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option>
+   <option value="bergerparker">bergerparker - Community diversity the Berger-Parker index</option>
+   <option value="coverage">coverage - Community diversity the sampling coverage </option>
+   <option value="goodscoverage">goodscoverage - Community diversity the Good's estimate of sampling coverage </option>
+   <option value="simpson" selected="true">simpson - Community diversity the Simpson index</option>
+   <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
+   <option value="qstat">qstat - Community diversity the Q statistic</option>
+   <option value="shannon" selected="true">shannon - Community diversity the Shannon index</option>
+   <option value="np_shannon" selected="true">np_shannon - Community diversity the non-parametric Shannon index</option>
+   <option value="boneh">boneh - Estimator Boneh's estimator</option>
+   <option value="efron">efron - Estimator Efron's estimator</option>
+   <option value="shen">shen - Estimator Shen's estimator</option>
+   <option value="solow">solow - Estimator Solow's estimator</option>
+   <option value="logseries">logseries - Statistical distribution tests whether observed data follow the log series distribution</option>
+   <option value="geometric">geometric - Statistical distribution tests whether observed data follow the geometric series distribution</option>
+   <option value="bstick">bstick - Statistical distribution tests whether observed data follow the broken stick distribution</option>
+   <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
   </param>
   <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs (default 10)"/>
   <param name="size" type="integer" value="0" label="size - sample size for OTU prediction (ignored if &lt; 1)" 
diff -r 697156806162 -r d86987601022 mothur/tools/mothur/dist.shared.xml
--- a/mothur/tools/mothur/dist.shared.xml	Tue Jan 17 11:22:44 2012 -0600
+++ b/mothur/tools/mothur/dist.shared.xml	Tue Jan 17 14:16:44 2012 -0600
@@ -52,12 +52,46 @@
    </options>
   </param>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult2" index="2"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult2" column="2" value="shar" />
-   </options>
+   <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
+   <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
+   <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
+   <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
+   <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
+   <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
+   <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
+   <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
+   <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
+   <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
+   <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
+   <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
+   <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
+   <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
+   <option value="hamming">hamming - Community Membership Similarity -</option>
+   <option value="memchi2">memchi2 - Community Membership Similarity -</option>
+   <option value="memchord">memchord - Community Membership Similarity -</option>
+   <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
+   <option value="mempearson">mempearson - Community Membership Similarity -</option>
+   <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
+   <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
+   <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
+   <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
+   <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
+   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option>
+   <option value="canberra">canberra - Community Structure Similarity -</option>
+   <option value="gower">gower - Community Structure Similarity -</option>
+   <option value="hellinger">hellinger - Community Structure Similarity -</option>
+   <option value="manhattan">manhattan - Community Structure Similarity -</option>
+   <option value="odum">odum - Community Structure Similarity -</option>
+   <option value="soergel">soergel - Community Structure Similarity -</option>
+   <option value="spearman">spearman - Community Structure Similarity -</option>
+   <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
+   <option value="structchi2">structchi2 - Community Structure Similarity -</option>
+   <option value="structchord">structchord - Community Structure Similarity -</option>
+   <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
+   <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
+   <option value="structpearson">structpearson - Community Structure Similarity -</option>
+   <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
+   <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
   </param>
   <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair">
    <option value="lt">Phylip formatted Lower Triangle Matrix</option>
diff -r 697156806162 -r d86987601022 mothur/tools/mothur/heatmap.sim.xml
--- a/mothur/tools/mothur/heatmap.sim.xml	Tue Jan 17 11:22:44 2012 -0600
+++ b/mothur/tools/mothur/heatmap.sim.xml	Tue Jan 17 14:16:44 2012 -0600
@@ -62,12 +62,16 @@
       </options>
      </param>
      <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-      <options from_file="mothur_calculators.loc">
-        <column name="mult2" index="2"/>
-        <column name="name" index="0"/>
-        <column name="value" index="0"/>
-        <filter type="static_value" name="mult2" column="2" value="shar" />
-      </options>
+      <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
+      <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
+      <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
+      <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
+      <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
+      <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
+      <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
+      <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
+      <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
+      <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option>
      </param>
    </when>
    <when value="column">
diff -r 697156806162 -r d86987601022 mothur/tools/mothur/rarefaction.shared.xml
--- a/mothur/tools/mothur/rarefaction.shared.xml	Tue Jan 17 11:22:44 2012 -0600
+++ b/mothur/tools/mothur/rarefaction.shared.xml	Tue Jan 17 14:16:44 2012 -0600
@@ -43,12 +43,8 @@
   <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/>
   <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult2" index="2"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult2" column="2" value="rare" />
-   </options>
+   <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option>
+   <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option>
   </param>
  </inputs>
  <outputs>
diff -r 697156806162 -r d86987601022 mothur/tools/mothur/rarefaction.single.xml
--- a/mothur/tools/mothur/rarefaction.single.xml	Tue Jan 17 11:22:44 2012 -0600
+++ b/mothur/tools/mothur/rarefaction.single.xml	Tue Jan 17 14:16:44 2012 -0600
@@ -45,12 +45,21 @@
    </options>
   </param>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult2" index="2"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult2" column="2" value="sing" />
-   </options>
+   <option value="ace">ace - Community richness the ACE estimator</option>
+   <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
+   <option value="chao">chao - Community richness the Chao1 estimator</option>
+   <option value="jack">jack - Community richness the jackknife estimator</option>
+   <option value="sobs" selected="true">sobs - Community richness the observed richness</option>
+   <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option>
+   <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option>
+   <option value="heip">heip - Community evenness Heip's metric of community evenness</option>
+   <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option>
+   <option value="coverage">coverage - Community diversity the sampling coverage </option>
+   <option value="simpson">simpson - Community diversity the Simpson index</option>
+   <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
+   <option value="shannon">shannon - Community diversity the Shannon index</option>
+   <option value="np_shannon">np_shannon - Community diversity the non-parametric Shannon index</option>
+   <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
   </param>
   <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/>
   <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/>
diff -r 697156806162 -r d86987601022 mothur/tools/mothur/summary.shared.xml
--- a/mothur/tools/mothur/summary.shared.xml	Tue Jan 17 11:22:44 2012 -0600
+++ b/mothur/tools/mothur/summary.shared.xml	Tue Jan 17 14:16:44 2012 -0600
@@ -40,12 +40,46 @@
    </options>
   </param>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult" index="1"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult" column="1" value="shared" />
-   </options>
+   <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
+   <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
+   <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
+   <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
+   <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
+   <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
+   <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
+   <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
+   <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
+   <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
+   <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
+   <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
+   <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
+   <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
+   <option value="hamming">hamming - Community Membership Similarity -</option>
+   <option value="memchi2">memchi2 - Community Membership Similarity -</option>
+   <option value="memchord">memchord - Community Membership Similarity -</option>
+   <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
+   <option value="mempearson">mempearson - Community Membership Similarity -</option>
+   <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
+   <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
+   <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
+   <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
+   <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
+   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option>
+   <option value="canberra">canberra - Community Structure Similarity -</option>
+   <option value="gower">gower - Community Structure Similarity -</option>
+   <option value="hellinger">hellinger - Community Structure Similarity -</option>
+   <option value="manhattan">manhattan - Community Structure Similarity -</option>
+   <option value="odum">odum - Community Structure Similarity -</option>
+   <option value="soergel">soergel - Community Structure Similarity -</option>
+   <option value="spearman">spearman - Community Structure Similarity -</option>
+   <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
+   <option value="structchi2">structchi2 - Community Structure Similarity -</option>
+   <option value="structchord">structchord - Community Structure Similarity -</option>
+   <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
+   <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
+   <option value="structpearson">structpearson - Community Structure Similarity -</option>
+   <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
+   <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
   </param>
   <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
   <param name="distance" type="boolean" truevalue="--distance=true" falsevalue="" checked="false" label="distance - Output a distance file for each calculator at each label"/>
diff -r 697156806162 -r d86987601022 mothur/tools/mothur/summary.single.xml
--- a/mothur/tools/mothur/summary.single.xml	Tue Jan 17 11:22:44 2012 -0600
+++ b/mothur/tools/mothur/summary.single.xml	Tue Jan 17 14:16:44 2012 -0600
@@ -44,12 +44,31 @@
    </options>
   </param>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult" index="1"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult" column="1" value="single" />
-   </options>
+   <option value="ace" selected="true">ace - Community richness the ACE estimator</option>
+   <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
+   <option value="chao" selected="true">chao - Community richness the Chao1 estimator</option>
+   <option value="jack" selected="true">jack - Community richness the jackknife estimator</option>
+   <option value="sobs" selected="true">sobs - Community richness the observed richness</option>
+   <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option>
+   <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option>
+   <option value="heip">heip - Community evenness Heip's metric of community evenness</option>
+   <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option>
+   <option value="bergerparker">bergerparker - Community diversity the Berger-Parker index</option>
+   <option value="coverage">coverage - Community diversity the sampling coverage </option>
+   <option value="goodscoverage">goodscoverage - Community diversity the Good's estimate of sampling coverage </option>
+   <option value="simpson" selected="true">simpson - Community diversity the Simpson index</option>
+   <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
+   <option value="qstat">qstat - Community diversity the Q statistic</option>
+   <option value="shannon" selected="true">shannon - Community diversity the Shannon index</option>
+   <option value="np_shannon" selected="true">np_shannon - Community diversity the non-parametric Shannon index</option>
+   <option value="boneh">boneh - Estimator Boneh's estimator</option>
+   <option value="efron">efron - Estimator Efron's estimator</option>
+   <option value="shen">shen - Estimator Shen's estimator</option>
+   <option value="solow">solow - Estimator Solow's estimator</option>
+   <option value="logseries">logseries - Statistical distribution tests whether observed data follow the log series distribution</option>
+   <option value="geometric">geometric - Statistical distribution tests whether observed data follow the geometric series distribution</option>
+   <option value="bstick">bstick - Statistical distribution tests whether observed data follow the broken stick distribution</option>
+   <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
   </param>
   <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/>
   <param name="size" type="integer" value="0" label="size - "/>
diff -r 697156806162 -r d86987601022 mothur/tools/mothur/tree.shared.xml
--- a/mothur/tools/mothur/tree.shared.xml	Tue Jan 17 11:22:44 2012 -0600
+++ b/mothur/tools/mothur/tree.shared.xml	Tue Jan 17 14:16:44 2012 -0600
@@ -71,12 +71,46 @@
    </when>
   </conditional>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult2" index="2"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult2" column="2" value="shar" />
-   </options>
+   <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
+   <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
+   <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
+   <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
+   <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
+   <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
+   <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
+   <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
+   <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
+   <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
+   <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
+   <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
+   <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
+   <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
+   <option value="hamming">hamming - Community Membership Similarity -</option>
+   <option value="memchi2">memchi2 - Community Membership Similarity -</option>
+   <option value="memchord">memchord - Community Membership Similarity -</option>
+   <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
+   <option value="mempearson">mempearson - Community Membership Similarity -</option>
+   <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
+   <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
+   <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
+   <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
+   <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
+   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option>
+   <option value="canberra">canberra - Community Structure Similarity -</option>
+   <option value="gower">gower - Community Structure Similarity -</option>
+   <option value="hellinger">hellinger - Community Structure Similarity -</option>
+   <option value="manhattan">manhattan - Community Structure Similarity -</option>
+   <option value="odum">odum - Community Structure Similarity -</option>
+   <option value="soergel">soergel - Community Structure Similarity -</option>
+   <option value="spearman">spearman - Community Structure Similarity -</option>
+   <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
+   <option value="structchi2">structchi2 - Community Structure Similarity -</option>
+   <option value="structchord">structchord - Community Structure Similarity -</option>
+   <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
+   <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
+   <option value="structpearson">structpearson - Community Structure Similarity -</option>
+   <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
+   <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
   </param>
  </inputs>
  <outputs>