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annotate mothur/tool-data/mothur_calulators.loc @ 11:2ab2418616af draft

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tool_dependencies.xml - now working, added chmod for uchime_src/mk, and changed move_file
author Jim Johnson <jj@umn.edu>
date Fri, 30 Nov 2012 10:51:36 -0600
parents 591e72edabed
children
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1 #This is a sample file distributed with Galaxy that enables
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2 # Mothur tools to present a choice of values for calculators
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3 # source - http://www.mothur.org/wiki/Calculators
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4 #file has this format (fields are separated by TAB characters):
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5 #
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6 # venn sobs,chao,ace sharedsobs,sharedchao,sharedace
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7 # rarefaction.shared sharednseqs,sharedobserved
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8 # rarefaction.single ace,bootstrap,chao,coverage,heip,invsimpson,jack,npshannon,nseqs,shannon,shannoneven,simpson,simpsoneven,smithwilson,sobs
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9 # dist.shared braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc
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10 # tree.shared braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc
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11 # heatmap.sim braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc
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12 # collect.shared anderberg,braycurtis,jabund,jclass,jest,kstest,kulczynski,kulczynskicody,lennon,morisitahorn,ochiai,sharedace,sharedchao,sharednseqs,sharedsobs,sorabund,sorclass,sorest,thetan,thetayc,whittaker
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13 # summary.shared anderberg,braycurtis,jabund,jclass,jest,kstest,kulczynski,kulczynskicody,lennon,morisitahorn,ochiai,sharedace,sharedchao,sharednseqs,sharedsobs,sorabund,sorclass,sorest,thetan,thetayc,whittaker
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14 # collect.single ace,bergerparker,boneh,bootstrap,bstick,chao,coverage,efron,geometric,goodscoverage,heip,invsimpson,jack,logseries,npshannon,nseqs,qstat,shannon,shannoneven,shen,simpson,simpsoneven,smithwilson,sobs,solow
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15 # summary.single ace,bergerparker,boneh,bootstrap,bstick,chao,coverage,efron,geometric,goodscoverage,heip,invsimpson,jack,logseries,npshannon,nseqs,qstat,shannon,shannoneven,shen,simpson,simpsoneven,smithwilson,sobs,solow
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16 #
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17 #<calculator> <mult> <mult2> <category> <description>
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18 #
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19 #Community richness
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20 sobs single sing Community richness the observed richness
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21 chao single sing Community richness the Chao1 estimator
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22 ace single sing Community richness the ACE estimator
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23 jack single sing Community richness the jackknife estimator
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24 bootstrap single sing Community richness the bootstrap estimator
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25 #Community diversity
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26 bergerparker single xxxx Community diversity the Berger-Parker index
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27 shannon single sing Community diversity the Shannon index
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28 npshannon single sing Community diversity the non-parametric Shannon index
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29 simpson single sing Community diversity the Simpson index
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30 simpsoneven single sing Community diversity the Simpson index
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31 invsimpson single sing Community diversity the Simpson index
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32 coverage single sing Community diversity the sampling coverage coverage
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33 qstat single xxxx Community diversity the Q statistic
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34 #Estimates of number of additional OTUs observed with extra sampling
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35 boneh single xxxx Estimator Boneh's estimator
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36 efron single xxxx Estimator Efron's estimator
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37 shen single xxxx Estimator Shen's estimator
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38 solow single xxxx Estimator Solow's estimator
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39 #Statistical distributions
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40 logseries single xxxx Statistical distribution tests whether observed data follow the log series distribution
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41 geometric single xxxx Statistical distribution tests whether observed data follow the geometric series distribution
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42 bstick single xxxx Statistical distribution tests whether observed data follow the broken stick distribution
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43 # Shared community richness
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44 sharedsobs shared xxxx Shared community richness the observed richness shared between two or more samples
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45 sharedchao shared xxxx Shared community richness the two or more sample shared Chao1 richness estimator
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46 sharedace shared xxxx Shared community richness the two sample shared ACE richness estimator
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47 #Similarity in community membership
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48 anderberg shared xxxx Community Membership Similarity the Anderberg similarity coefficient
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49 jclass shared shar Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness
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50 jest shared shar Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses
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51 kulczynski shared xxxx Community Membership Similarity the Kulczynski similarity coefficient
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52 kulczynskicody shared xxxx Community Membership Similarity the Kulczynski-Cody similarity coefficient
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53 lennon shared xxxx Community Membership Similarity the Lennon similarity coefficient
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54 ochiai shared xxxx Community Membership Similarity the Ochiai similarity coefficient
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55 sorclass shared shar Community Membership Similarity the Sorenson similarity coefficient based on the observed richness
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56 sorest shared shar Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses
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57 whittaker shared xxxx Community Membership Similarity the Whittaker similarity coefficient
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58 #Similarity in community structure
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59 braycurtis shared shar Community Structure Similarity the Bray-Curtis similarity coefficient
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60 jabund shared shar Community Structure Similarity the abundance-based Jaccard similarity coefficient
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61 morisitahorn shared shar Community Structure Similarity the Morisita-Horn similarity coefficient
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62 sorabund shared shar Community Structure Similarity the abundance-based Sorenson similarity coefficient
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63 thetan shared shar Community Structure Similarity the Smith theta similarity coefficient
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64 thetayc shared shar Community Structure Similarity the Yue & Clayton theta similarity coefficient
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65 #Utility calculators
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66 nseqs single sing Utility the number of sequences in a sample
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67 sharednseqs shared rare Utility the number of sequences in two samples
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68 sharedobserved shared rare Utility the number of sequences in two samples