Mercurial > repos > jjohnson > mothur_toolsuite
changeset 19:d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 17 Jan 2012 14:16:44 -0600 |
| parents | 697156806162 |
| children | fb3a03cdc2c8 |
| files | mothur/tool-data/mothur_calculators.loc mothur/tool-data/mothur_calculators.loc.sample mothur/tools/mothur/collect.shared.xml mothur/tools/mothur/collect.single.xml mothur/tools/mothur/dist.shared.xml mothur/tools/mothur/heatmap.sim.xml mothur/tools/mothur/rarefaction.shared.xml mothur/tools/mothur/rarefaction.single.xml mothur/tools/mothur/summary.shared.xml mothur/tools/mothur/summary.single.xml mothur/tools/mothur/tree.shared.xml |
| diffstat | 11 files changed, 237 insertions(+), 251 deletions(-) [+] |
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--- 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
--- 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
--- 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>
--- 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 < 1)"
--- 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>
--- 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">
--- 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>
--- 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"/>
--- 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"/>
--- 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 - "/>
--- 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>