# HG changeset patch # User Jim Johnson # Date 1320774332 21600 # Node ID a6189f58fedb5bca12eb5c73b39c525f9cf4ae83 # Parent ee59e5cff3ba96de9b3025d1bfebaf542122e987 Mothur - updated for Mothur version 1.22.0 diff -r ee59e5cff3ba -r a6189f58fedb mothur/README --- a/mothur/README Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/README Tue Nov 08 11:45:32 2011 -0600 @@ -1,7 +1,9 @@ Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page -Install mothur v.1.20.0 on your galaxy system so galaxy can execute the mothur command - ( This version of wrappers is designed for Mothur version 1.19 - it may work on later versions ) +(The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands) + +Install mothur v.1.22.0 on your galaxy system so galaxy can execute the mothur command + ( This version of wrappers is designed for Mothur version 1.22 - it may work on later versions ) http://www.mothur.org/wiki/Download_mothur http://www.mothur.org/wiki/Installation ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode ) @@ -45,6 +47,8 @@ SILVA-compatible mask: - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter + Lookup Files for sff flow analysis using shhh.flows: + http://www.mothur.org/wiki/Alignment_database Example from UMN installation: (We also made these available in a Galaxy public data library) /project/db/galaxy/mothur/Silva.bacteria.zip @@ -117,6 +121,9 @@ + + + @@ -127,6 +134,7 @@ + @@ -138,10 +146,13 @@ + + + @@ -169,6 +180,7 @@ + @@ -200,6 +212,7 @@ + @@ -235,10 +248,11 @@ - ############ DESIGN NOTES ######################################################################################################### Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py + (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands) + * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name. * Every tool will produce the logfile of the mothur run as an output. * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py diff -r ee59e5cff3ba -r a6189f58fedb mothur/lib/galaxy/datatypes/metagenomics.py --- a/mothur/lib/galaxy/datatypes/metagenomics.py Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/lib/galaxy/datatypes/metagenomics.py Tue Nov 08 11:45:32 2011 -0600 @@ -722,7 +722,57 @@ close(fh) return False -class SequenceTaxonomy(Tabular): +class RefTaxonomy(Tabular): + file_ext = 'ref.taxonomy' + """ + A table with 2 or 3 columns: + - SequenceName + - Taxonomy (semicolon-separated taxonomy in descending order) + - integer ? + Example: 2-column ( http://www.mothur.org/wiki/Taxonomy_outline ) + X56533.1 Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma; + X97975.1 Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida; + AF052717.1 Eukaryota;Parabasalidea; + Example: 3-column ( http://vamps.mbl.edu/resources/databases.php ) + v3_AA008 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus 5 + v3_AA016 Bacteria 120 + v3_AA019 Archaea;Crenarchaeota;Marine_Group_I 1 + """ + def __init__(self, **kwd): + Tabular.__init__( self, **kwd ) + self.column_names = ['name','taxonomy'] + + def sniff( self, filename ): + """ + Determines whether the file is a SequenceTaxonomy + """ + try: + pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?)*(;)?)$' + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + if not line: + break #EOF + line = line.strip() + if line: + fields = line.split('\t') + if 2 <= len(fields) <= 3: + return False + if not re.match(pat,fields[1]): + return False + count += 1 + if count > 10: + break + if count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class SequenceTaxonomy(RefTaxonomy): file_ext = 'seq.taxonomy' """ A table with 2 columns: @@ -933,6 +983,57 @@ fh.close() return False +class SffFlow(Tabular): + MetadataElement( name="flow_values", default="", no_value="", optional=True , desc="Total number of flow values", readonly=True) + MetadataElement( name="flow_order", default="TACG", no_value="TACG", desc="Total number of flow values", readonly=False) + file_ext = 'sff.flow' + """ + The first line is the total number of flow values - 800 for Titanium data. For GS FLX it would be 400. + Following lines contain: + - SequenceName + - the number of useable flows as defined by 454's software + - the flow intensity for each base going in the order of TACG. + Example: + 800 + GQY1XT001CQL4K 85 1.04 0.00 1.00 0.02 0.03 1.02 0.05 ... + GQY1XT001CQIRF 84 1.02 0.06 0.98 0.06 0.09 1.05 0.07 ... + GQY1XT001CF5YW 88 1.02 0.02 1.01 0.04 0.06 1.02 0.03 ... + """ + def __init__(self, **kwd): + Tabular.__init__( self, **kwd ) + + def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ): + Tabular.set_meta(self, dataset, overwrite, 1, max_data_lines) + try: + fh = open( filename ) + line = fh.readline() + line = line.strip() + flow_values = int(line) + dataset.metadata.flow_values = flow_values + finally: + fh.close() + + def make_html_table( self, dataset, skipchars=[] ): + """Create HTML table, used for displaying peek""" + out = [''] + comments = [] + try: + # Generate column header + out.append('') + out.append( '' % 1 ) + out.append( '' % 2 ) + for i in range( 3, dataset.metadata.columns+1 ): + base = dataset.metadata.flow_order[(i+1)%4] + out.append( '' % (i-2,base) ) + out.append('') + out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) + out.append( '

%d. Name	%d. Flows	%d. %d %s

' ) + out = "".join( out ) + except Exception, exc: + out = "Can't create peek %s" % str( exc ) + return out + + ## Qiime Classes class QiimeMetadataMapping(Tabular): diff -r ee59e5cff3ba -r a6189f58fedb mothur/tool-data/mothur_aligndb.loc --- a/mothur/tool-data/mothur_aligndb.loc Wed Oct 05 10:37:11 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of metagenomics files. -#file has this format (white space characters are TAB characters): -# -# -# -greengenes /project/db/galaxy/mothur/core_set_aligned.imputed.fasta -silva archaea /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta -silva bacteria /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta -silva eukarya /project/db/galaxy/mothur/silva.eukarya.fasta -silva archaea nogap /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta -silva bacteria nogap /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta -silva eukarya nogap /project/db/galaxy/mothur/nogap.eukarya.fasta - diff -r ee59e5cff3ba -r a6189f58fedb mothur/tool-data/mothur_aligndb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tool-data/mothur_aligndb.loc.sample Tue Nov 08 11:45:32 2011 -0600 @@ -0,0 +1,16 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters): +# +# Reference Alignments: http://www.mothur.org/wiki/Alignment_database +# +# +# +greengenes /project/db/galaxy/mothur/core_set_aligned.imputed.fasta +silva archaea /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta +silva bacteria /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta +silva eukarya /project/db/galaxy/mothur/silva.eukarya.fasta +silva archaea nogap /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta +silva bacteria nogap /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta +silva eukarya nogap /project/db/galaxy/mothur/nogap.eukarya.fasta + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tool-data/mothur_calculators.loc --- a/mothur/tool-data/mothur_calculators.loc Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/tool-data/mothur_calculators.loc Tue Nov 08 11:45:32 2011 -0600 @@ -1,6 +1,8 @@ #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): # ## diff -r ee59e5cff3ba -r a6189f58fedb mothur/tool-data/mothur_calculators.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tool-data/mothur_calculators.loc.sample Tue Nov 08 11:45:32 2011 -0600 @@ -0,0 +1,98 @@ +#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 +# +## +# +# +##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 ee59e5cff3ba -r a6189f58fedb mothur/tool-data/mothur_calulators.loc --- a/mothur/tool-data/mothur_calulators.loc Wed Oct 05 10:37:11 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -#This is a sample file distributed with Galaxy that enables -# Mothur tools to present a choice of values for calculators -# source - http://www.mothur.org/wiki/Calculators -#file has this format (fields are separated by TAB characters): -# -# venn sobs,chao,ace sharedsobs,sharedchao,sharedace -# rarefaction.shared sharednseqs,sharedobserved -# rarefaction.single ace,bootstrap,chao,coverage,heip,invsimpson,jack,npshannon,nseqs,shannon,shannoneven,simpson,simpsoneven,smithwilson,sobs -# dist.shared braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc -# tree.shared braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc -# heatmap.sim braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc -# collect.shared anderberg,braycurtis,jabund,jclass,jest,kstest,kulczynski,kulczynskicody,lennon,morisitahorn,ochiai,sharedace,sharedchao,sharednseqs,sharedsobs,sorabund,sorclass,sorest,thetan,thetayc,whittaker -# summary.shared anderberg,braycurtis,jabund,jclass,jest,kstest,kulczynski,kulczynskicody,lennon,morisitahorn,ochiai,sharedace,sharedchao,sharednseqs,sharedsobs,sorabund,sorclass,sorest,thetan,thetayc,whittaker -# collect.single ace,bergerparker,boneh,bootstrap,bstick,chao,coverage,efron,geometric,goodscoverage,heip,invsimpson,jack,logseries,npshannon,nseqs,qstat,shannon,shannoneven,shen,simpson,simpsoneven,smithwilson,sobs,solow -# summary.single ace,bergerparker,boneh,bootstrap,bstick,chao,coverage,efron,geometric,goodscoverage,heip,invsimpson,jack,logseries,npshannon,nseqs,qstat,shannon,shannoneven,shen,simpson,simpsoneven,smithwilson,sobs,solow -# -# -# -#Community richness -sobs single sing Community richness the observed richness -chao single sing Community richness the Chao1 estimator -ace single sing Community richness the ACE estimator -jack single sing Community richness the jackknife estimator -bootstrap single sing Community richness the bootstrap estimator -#Community diversity -bergerparker single xxxx Community diversity the Berger-Parker index -shannon single sing Community diversity the Shannon index -npshannon single sing Community diversity the non-parametric Shannon index -simpson single sing Community diversity the Simpson index -simpsoneven single sing Community diversity the Simpson index -invsimpson single sing Community diversity the Simpson index -coverage single sing Community diversity the sampling coverage coverage -qstat single xxxx Community diversity the Q statistic -#Estimates of number of additional OTUs observed with extra sampling -boneh single xxxx Estimator Boneh's estimator -efron single xxxx Estimator Efron's estimator -shen single xxxx Estimator Shen's estimator -solow single xxxx Estimator Solow's estimator -#Statistical distributions -logseries single xxxx Statistical distribution tests whether observed data follow the log series distribution -geometric single xxxx Statistical distribution tests whether observed data follow the geometric series distribution -bstick single xxxx Statistical distribution tests whether observed data follow the broken stick distribution -# Shared community richness -sharedsobs shared xxxx Shared community richness the observed richness shared between two or more samples -sharedchao shared xxxx Shared community richness the two or more sample shared Chao1 richness estimator -sharedace shared xxxx Shared community richness the two sample shared ACE richness estimator -#Similarity in community membership -anderberg shared xxxx Community Membership Similarity the Anderberg similarity coefficient -jclass shared shar Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness -jest shared shar Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses -kulczynski shared xxxx Community Membership Similarity the Kulczynski similarity coefficient -kulczynskicody shared xxxx Community Membership Similarity the Kulczynski-Cody similarity coefficient -lennon shared xxxx Community Membership Similarity the Lennon similarity coefficient -ochiai shared xxxx Community Membership Similarity the Ochiai similarity coefficient -sorclass shared shar Community Membership Similarity the Sorenson similarity coefficient based on the observed richness -sorest shared shar Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses -whittaker shared xxxx Community Membership Similarity the Whittaker similarity coefficient -#Similarity in community structure -braycurtis shared shar Community Structure Similarity the Bray-Curtis similarity coefficient -jabund shared shar Community Structure Similarity the abundance-based Jaccard similarity coefficient -morisitahorn shared shar Community Structure Similarity the Morisita-Horn similarity coefficient -sorabund shared shar Community Structure Similarity the abundance-based Sorenson similarity coefficient -thetan shared shar Community Structure Similarity the Smith theta similarity coefficient -thetayc shared shar Community Structure Similarity the Yue & Clayton theta similarity coefficient -#Utility calculators -nseqs single sing Utility the number of sequences in a sample -sharednseqs shared rare Utility the number of sequences in two samples -sharedobserved shared rare Utility the number of sequences in two samples diff -r ee59e5cff3ba -r a6189f58fedb mothur/tool-data/mothur_lookup.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tool-data/mothur_lookup.loc.sample Tue Nov 08 11:45:32 2011 -0600 @@ -0,0 +1,13 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters): +# +# lookup files from: http://www.mothur.org/wiki/Lookup_files +# +# +# +GS20 /project/db/galaxy/mothur/lookup/LookUp_GS20.pat +GSFLX /project/db/galaxy/mothur/lookup/LookUp_GSFLX.pat +Titanium /project/db/galaxy/mothur/lookup/LookUp_Titanium.pat + + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tool-data/mothur_map.loc --- a/mothur/tool-data/mothur_map.loc Wed Oct 05 10:37:11 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of metagenomics files. -#file has this format (white space characters are TAB characters): -# -# -# -greengenes /project/db/galaxy/mothur/gg.ss.map -silva /project/db/galaxy/mothur/silva.ss.map diff -r ee59e5cff3ba -r a6189f58fedb mothur/tool-data/mothur_map.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tool-data/mothur_map.loc.sample Tue Nov 08 11:45:32 2011 -0600 @@ -0,0 +1,10 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters): +# +# Secondary structure maps: http://www.mothur.org/wiki/Secondary_structure_map +# +# +# +greengenes /project/db/galaxy/mothur/gg.ss.map +silva /project/db/galaxy/mothur/silva.ss.map diff -r ee59e5cff3ba -r a6189f58fedb mothur/tool-data/mothur_taxonomy.loc --- a/mothur/tool-data/mothur_taxonomy.loc Wed Oct 05 10:37:11 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of metagenomics files. -#file has this format (white space characters are TAB characters): -# -# -# -archaea.gg /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax -archaea.silva /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax -archaea.rdp /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax -archaea.ncbi /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax -bacteria.gg /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax -bacteria.silva /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax -bacteria.ncbi /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax -bacteria.rdp /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax -bacteria.rdp6 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax -eukarya.silva /project/db/galaxy/mothur/silva.eukarya.silva.tax -eukarya.ncbi /project/db/galaxy/mothur/silva.eukarya.ncbi.tax - diff -r ee59e5cff3ba -r a6189f58fedb mothur/tool-data/mothur_taxonomy.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tool-data/mothur_taxonomy.loc.sample Tue Nov 08 11:45:32 2011 -0600 @@ -0,0 +1,20 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters): +# +# Silva reference files: http://www.mothur.org/wiki/Silva_reference_files +# +# +# +archaea.gg /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax +archaea.silva /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax +archaea.rdp /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax +archaea.ncbi /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax +bacteria.gg /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax +bacteria.silva /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax +bacteria.ncbi /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax +bacteria.rdp /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax +bacteria.rdp6 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax +eukarya.silva /project/db/galaxy/mothur/silva.eukarya.silva.tax +eukarya.ncbi /project/db/galaxy/mothur/silva.eukarya.ncbi.tax + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/chimera.slayer.xml --- a/mothur/tools/mothur/chimera.slayer.xml Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/tools/mothur/chimera.slayer.xml Tue Nov 08 11:45:32 2011 -0600 @@ -1,4 +1,4 @@ - + Find putative chimeras using slayer mothur_wrapper.py @@ -12,6 +12,9 @@ #if $alignment.name.__str__ != "None" and len($alignment.name.__str__) > 0: --name=$alignment.name #end if + #if $alignment.group.__str__ != '': + --group=$alignment.group + #end if #else: --reference=$alignment.template #end if @@ -56,6 +59,8 @@ + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/chimera.uchime.xml --- a/mothur/tools/mothur/chimera.uchime.xml Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/tools/mothur/chimera.uchime.xml Tue Nov 08 11:45:32 2011 -0600 @@ -1,4 +1,4 @@ - + Find putative chimeras using uchime mothur_wrapper.py @@ -23,6 +23,9 @@ #if float($template.abskew.__str__) > 0: --abskew=$template.abskew #end if + #if $template.group.__str__ != '': + --group=$template.group + #end if #elif $template.source == 'names': --name=$template.name #end if @@ -95,6 +98,9 @@ + + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/cluster.split.xml --- a/mothur/tools/mothur/cluster.split.xml Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/tools/mothur/cluster.split.xml Tue Nov 08 11:45:32 2011 -0600 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices mothur_wrapper.py @@ -80,7 +80,7 @@ - @@ -90,7 +90,7 @@ + help="Ignore pairwise distances larger than this, a common value would be 0.25"/> + counts the number of sequences represented by a specific group or set of groups + + mothur_wrapper.py + --cmd='count.groups' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.groups.count$:'$grp_count + --outputdir='$logfile.extra_files_path' + #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): + --shared=$group + #else: + --group=$group + #end if + #if $groupnames.source == 'groups': + #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: + --groups=$groupnames.groups + #end if + #elif $groupnames.source == 'accnos': + #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0: + --accnos=$groupnames.accnos + #end if + #end if + + + + + + + + + + + + All groups displayed if none are selected. + + + + + + + + + + + + + + + + + + mothur + + + + +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file. + +.. _shared: http://www.mothur.org/wiki/Shared_file +.. _group: http://www.mothur.org/wiki/Group_file +.. _count.groups: http://www.mothur.org/wiki/Count.groups + + + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/make.shared.xml --- a/mothur/tools/mothur/make.shared.xml Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/tools/mothur/make.shared.xml Tue Nov 08 11:45:32 2011 -0600 @@ -1,4 +1,4 @@ - + Make a shared file from a list and a group mothur_wrapper.py @@ -18,9 +18,11 @@ #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if + #* #if $ordergroup.__str__ != "None" and len($ordergroup.__str__) > 0: --ordergroup=$ordergroup #end if + *# @@ -39,7 +41,9 @@ + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/mothur_wrapper.py --- a/mothur/tools/mothur/mothur_wrapper.py Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/tools/mothur/mothur_wrapper.py Tue Nov 08 11:45:32 2011 -0600 @@ -4,7 +4,7 @@ http://www.mothur.org/ Supports mothur version -mothur v.1.20.0 +mothur v.1.22.0 Class encapsulating Mothur galaxy tool. Expect each invocation to include: @@ -186,8 +186,8 @@ cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','save','processors']}) cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','save','processors']}) cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','save','processors']}) - cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','reference'], 'optional' : ['name','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','blastlocation','save','processors']}) - cmd_dict['chimera.uchime'] = dict({'required' : ['fasta'], 'optional' : ['name','reference','abskew','chimealns','minh','mindiv','xn','dn','xa','chunks','minchunk','idsmoothwindow','minsmoothid','maxp','skipgaps','skipgaps2','minlen','maxlen','ucl','queryfract','processors']}) + cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','reference'], 'optional' : ['name','group','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','blastlocation','save','processors']}) + cmd_dict['chimera.uchime'] = dict({'required' : ['fasta'], 'optional' : ['name','group','reference','abskew','chimealns','minh','mindiv','xn','dn','xa','chunks','minchunk','idsmoothwindow','minsmoothid','maxp','skipgaps','skipgaps2','minlen','maxlen','ucl','queryfract','processors']}) cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['countgaps','keep','short']}) cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']}) cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','save','processors']}) @@ -201,6 +201,7 @@ cmd_dict['collect.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','size','label','freq']}) cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label','cutoff']}) cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']}) + cmd_dict['count.groups'] = dict({'required' : ['group','shared'], 'optional' : ['accnos','groups']}) cmd_dict['count.seqs'] = dict({'required' : ['name'], 'optional' : ['group','groups']}) cmd_dict['degap.seqs'] = dict({'required' : ['fasta']}) cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []}) @@ -229,7 +230,7 @@ cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]}) cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []}) cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []}) - cmd_dict['make.shared'] = dict({'required' : ['list','group'], 'optional' : ['label','groups','ordergroup']}) + cmd_dict['make.shared'] = dict({'required' : ['list','group'], 'optional' : ['label','groups']}) cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']}) cmd_dict['merge.files'] = dict({'required' : ['input','output']}) cmd_dict['merge.groups'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label']}) @@ -244,7 +245,7 @@ cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']}) cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']}) cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']}) - cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs']}) + cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs','group']}) cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble']}) cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']}) cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy']}) @@ -255,14 +256,22 @@ cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']}) cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']}) cmd_dict['sens.spec'] = dict({'required' : ['list',['column','phylip']] , 'optional' : ['label','cutoff','hard','precision']}) + + cmd_dict['seq.error'] = dict({'required' : ['fasta','reference'] , 'optional' : ['name','qfile','report','ignorechimeras','threshold','processors']}) + cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']}) + + cmd_dict['shhh.flows'] = dict({'required' : [['flow','files']], 'optional' : ['lookup','maxiter','mindelta','cutoff','sigma','order','processors']}) + cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']}) cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']}) cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']}) cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']}) cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']}) cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']}) + cmd_dict['summary.tax'] = dict({'required' : ['taxonomy'], 'optional' : ['name','group','reftaxonomy']}) cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']}) + cmd_dict['trim.flows'] = dict({'required' : ['flow'], 'optional' : ['oligos','bdiffs','pdiffs','tdiffs','minflows','maxflows','fasta','signal','noise','maxhomop','order','processors']}) cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast','processors']}) cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']}) cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']}) @@ -316,6 +325,7 @@ parser.add_option( '--rollaverage', dest='rollaverage', type="int", help='Remove sequences that have a average quality below the value in a rolling window' ) parser.add_option( '--qstepsize', dest='qstepsize', type="int", help='Distance to move a rolling window for each step' ) parser.add_option( '--qtrim', dest='qtrim', help='For sequence below qthreshold, false to scrap file, true to trimmed and in trim file' ) + parser.add_option( '--ignorechimeras', dest='ignorechimeras', help='ignorechimeras' ) parser.add_option( '--flip', dest='flip', help='If true, reverse complement the sequences' ) parser.add_option( '--maxambig', dest='maxambig', type="int", help='Number of ambiguous base calls to allow' ) parser.add_option( '--maxhomop', dest='maxhomop', type="int", help='Maximun homopolymer length allowed' ) @@ -333,6 +343,7 @@ parser.add_option( '--group', dest='group', help='A file containing a list of names' ) parser.add_option( '--list', dest='list', help='A file containing a list of names' ) parser.add_option( '--alignreport', dest='alignreport', help='A align.report file ' ) + parser.add_option( '--report', dest='report', help='' ) parser.add_option( '--taxonomy', dest='taxonomy', help='A Taxonomy file' ) parser.add_option( '--reftaxonomy', dest='reftaxonomy', help='A Taxonomy file' ) parser.add_option( '--taxon', dest='taxon', help='A Taxon' ) @@ -383,6 +394,7 @@ parser.add_option( '--all', dest='all', help='Calculate for all' ) parser.add_option( '--freq', dest='freq', type="float", help='Frequency of sequences to choose, as fraction is 0.0 - 1.0 or iteration if int > 1' ) parser.add_option( '--iters', dest='iters', type='int', help='Iterations of randomizations' ) + parser.add_option( '--maxiter', dest='maxiter', type='int', help='Iterations' ) parser.add_option( '--maxiters', dest='maxiters', type='int', help='Iterations of randomizations' ) parser.add_option( '--jumble', dest='jumble', help='If false, just a collector curve across the samples' ) parser.add_option( '--conservation', dest='conservation', help='Template frequency information' ) @@ -400,6 +412,15 @@ parser.add_option( '--svg', dest='svg', help='SVG' ) parser.add_option( '--sfftxt', dest='sfftxt', help='Generate a sff.txt file' ) parser.add_option( '--flow', dest='flow', help='Generate a flowgram file' ) + parser.add_option( '--minflows', dest='minflows', type='int', help='the minimum number of flows that each sequence must contain' ) + parser.add_option( '--maxflows', dest='maxflows', type='int', help='the number of flows after which all other flows should be ignored.' ) + parser.add_option( '--signal', dest='signal', type='float', help='threshold for intensity to be signal' ) + parser.add_option( '--noise', dest='noise', type='float', help='threshold for intensity to be noise' ) + parser.add_option( '--mindelta', dest='mindelta', type='float', help='threshold for determining how much change in the flowgram correction' ) + parser.add_option( '--sigma', dest='sigma', type='float', help='sigma option is used to set the dispersion of the data in the expectation-maximization' ) + parser.add_option( '--order', dest='order', help='flow order e.g. TACG' ) + parser.add_option( '--lookup', dest='lookup', help='lookup file that are needed to run shhh.seqs' ) + parser.add_option( '--trim', dest='trim', help='Whether sequences and quality scores are trimmed to the clipQualLeft and clipQualRight values' ) parser.add_option( '--input', dest='input', help='' ) parser.add_option( '--phylip', dest='phylip', help='' ) diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/pre.cluster.xml --- a/mothur/tools/mothur/pre.cluster.xml Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/tools/mothur/pre.cluster.xml Tue Nov 08 11:45:32 2011 -0600 @@ -1,4 +1,4 @@ - + Remove sequences due to pyrosequencing errors mothur_wrapper.py @@ -13,6 +13,9 @@ #if $name.__str__ != "None" and len($name.__str__) > 0: --name=$name #end if + #if $group.__str__ != "None" and len($group.__str__) > 0: + --group=$group + #end if #if 20 >= int($diffs.__str__) >= 0: --diffs=$diffs #end if @@ -21,6 +24,7 @@ + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/seq.error.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/seq.error.xml Tue Nov 08 11:45:32 2011 -0600 @@ -0,0 +1,172 @@ + + assess error rates in sequencing data + + mothur_wrapper.py + #import re, os.path + #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] + #if 'summary' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.summary$:'" + $summary_out.__str__] + #end if + #if 'seq' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.seq$:'" + $seq_out.__str__] + #end if + #if 'seq_forward' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.seq.forward$:'" + $seq_forward_out.__str__] + #end if + #if 'seq_reverse' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.seq.reverse$:'" + $seq_reverse_out.__str__] + #end if + #if 'chimera' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.chimera$:'" + $chimera_out.__str__] + #end if + #if 'count' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.count$:'" + $count_out.__str__] + #end if + #if 'matrix' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.matrix$:'" + $matrix_out.__str__] + #end if + #if 'ref_query' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.ref-query$:'" + $ref_query_out.__str__] + #end if + --cmd='seq.error' + --outputdir='$logfile.extra_files_path' + --fasta=$fasta_in + --reference=$alignment.template + #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: + --name=$name_in + #end if + #if $qual.use.__str__ == 'yes': + --qfile=$qfile_in + --alignreport=$alignreport_in + #if 'quality' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.quality$:'" + $quality_out.__str__] + #end if + #if 'qual_forward' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.qual.forward$:'" + $qual_forward_out.__str__] + #end if + #if 'qual_reverse' in $output_sel.__str__.split(','): + #set results = $results + ["'^\S+.error.qual.reverse$:'" + $qual_reverse_out.__str__] + #end if + #end if + #if $threshold.__str__ != '': + --threshold=$threshold + #end if + $ignorechimeras + --result=#echo ','.join($results) + --processors=8 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ('summary' in output_sel) + + + ('seq' in output_sel) + + + ('seq_forward' in output_sel) + + + ('seq_reverse' in output_sel) + + + ('chimera' in output_sel) + + + ('count' in output_sel) + + + ('matrix' in output_sel) + + + ('quality' in output_sel) + + + ('qual_forward' in output_sel) + + + ('qual_reverse' in output_sel) + + + ('ref_query' in output_sel) + + + + mothur + + + + +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_. +This is demonstrated in http://www.mothur.org/wiki/Schloss_SOP#Error_analysis + +.. _template_alignment: http://www.mothur.org/wiki/Alignment_database +.. _seq.error: http://www.mothur.org/wiki/Seq.error + + + + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/sffinfo.xml --- a/mothur/tools/mothur/sffinfo.xml Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/tools/mothur/sffinfo.xml Tue Nov 08 11:45:32 2011 -0600 @@ -48,7 +48,7 @@ sfftxt == True - + flow == True diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/shhh.flows.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/shhh.flows.xml Tue Nov 08 11:45:32 2011 -0600 @@ -0,0 +1,103 @@ + + Denoise flowgrams (PyroNoise algorithm) + + mothur_wrapper.py + #import re, os.path + --cmd='shhh.flows' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shhh\.fasta$:'$shhh_fasta,'^\S+\.shhh\.qual$:'$shhh_qual,'^\S+\.shhh\.names$:'$shhh_names,'^\S+\.shhh\.groups$:'$shhh_groups,'^\S+\.shhh\.counts$:'$shhh_counts + --outputdir='$logfile.extra_files_path' + --flow=$flow + --lookup=$prob.lookup + #if $maxiter.__str__ != '': + --maxiter=$maxiter + #end if + #if $mindelta.__str__ != '': + --mindelta=$mindelta + #end if + #if $cutoff.__str__ != '': + --cutoff=$cutoff + #end if + #if $sigma.__str__ != '': + --sigma=$sigma + #end if + #if $order.__str__.strip() != '': + --order=$order + #end if + --processors=8 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mothur + + + + +**mothur overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The shhh.flows_ command is Pat Schloss's translation of Chris Quince's PyroNoise algorithm [1] from C to C++ with the incorporation of mothur's bells and whistles. Based on processing of test datasets provided by Quince, shhh.flows gives the same/similar output to AmpliconNoise. shhh.flows uses a expectation-maximization algorithm to correct flowgrams to identify the idealized form of each flowgram and translate that flowgram to a DNA sequence. Our testing has shown that when Titanium data are trimmed to 450 flows using trim.flows, shhh.flows provides the highest quality data for any other method available. In contrast, when we use the min/max number of flows suggested by Quince of 360/720, the error rate is not that great. This much improved error rate does come at a computational cost. Whereas the features in trim.seqs take on the order of minutes, shhh.flows can take on the order of hours. You will also need a lookup file that tells shhh.flows the probability of observing an intensity value for a given homopolymer length. You can get mothur-compatible files at: http://www.mothur.org/wiki/Lookup_files + +.. _shhh.flows: http://www.mothur.org/wiki/Shhh.flows + + + + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/sub.sample.xml --- a/mothur/tools/mothur/sub.sample.xml Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/tools/mothur/sub.sample.xml Tue Nov 08 11:45:32 2011 -0600 @@ -1,4 +1,4 @@ - + Create a sub sample mothur_wrapper.py @@ -12,7 +12,7 @@ #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.subsample\\.\2',$os.path.basename($input.fasta_in.__str__)) + ":'" + $fasta_out.__str__] #if $input.name_in.__str__ != "None" and len($input.name_in.__str__) > 0: --name=$input.name_in - ## #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.subsample\\.\2',$os.path.basename($input.name_in.__str__)) + ":'" + $names_out.__str__] + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.subsample\\.\2',$os.path.basename($input.name_in.__str__)) + ":'" + $names_out.__str__] #end if #if $input.use_group.to_filter == "yes": #if $input.use_group.group_in.__str__ != "None" and len($input.use_group.group_in.__str__) > 0: @@ -183,10 +183,10 @@ input['format'] == 'rabund' (input['format'] == 'fasta' and input['name_in'] != None) - --> ((input['format'] == 'fasta' or input['format'] == 'list') and input['use_group'] == 'yes') diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/summary.tax.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/summary.tax.xml Tue Nov 08 11:45:32 2011 -0600 @@ -0,0 +1,84 @@ + + Assign sequences to taxonomy + + mothur_wrapper.py + --cmd='summary.tax' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tax\.summary$:'$tax_summary + --outputdir='$logfile.extra_files_path' + --taxonomy=$tax.taxonomy + #if $name.__str__ != "None" and len($name.__str__) > 0: + --name='$name' + #end if + #if $group.__str__ != "None" and len($group.__str__) > 0: + --group='$group' + #end if + #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0: + --reftaxonomy=$reftax.taxonomy + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mothur + + + + +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information. + +.. _summary.tax: http://www.mothur.org/wiki/Summary.otu + + + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/trim.flows.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/trim.flows.xml Tue Nov 08 11:45:32 2011 -0600 @@ -0,0 +1,127 @@ + + partition by barcode, trim to length, cull by lenght and mismatches + + mothur_wrapper.py + #import re, os.path + --cmd='trim.flows' + ## #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] + ## #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($flow.__str__)) + ":'" + $trim_flow.__str__] + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.trim\.flow$:'$trim_flow, '^\S+\.scrap\.flow$:'$scrap_flow,'^\S+\.flow\.files$:'$flow_files,'^\S+\.flow\.fasta$:'$flow_fasta + --outputdir='$logfile.extra_files_path' + --flow=$flow + #if $minflows.__str__ != '': + --minflows=$minflows + #end if + #if $maxflows.__str__ != '': + --maxflows=$maxflows + #end if + #if $maxhomop.__str__ != '': + --maxhomop=$maxhomop + #end if + #if $order.__str__.strip() != '': + --order=$order + #end if + #if $signal.__str__ != '' + --signal=$signal + #end if + #if $noise.__str__ != '' + --noise=$noise + #end if + #if $oligo.add == "yes": + --oligos=$oligo.oligos + #if int($oligo.bdiffs.__str__) > 0: + --bdiffs=$oligo.bdiffs + #end if + #if int($oligo.pdiffs.__str__) > 0: + --pdiffs=$oligo.pdiffs + #end if + #if int($oligo.tdiffs.__str__) > 0: + --tdiffs=$oligo.tdiffs + #end if + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.(\S+\.flow)$:sff.flow' + #end if + $fasta + --processors=8 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oligos != None + + + fasta == True + + + + mothur + + + + +**mothur overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The trim.flows_ command is analogous to the trim.seqs command, except that it uses the flowgram data that comes bundled in the sff file that is generated by 454 sequencing. It's primary usage is as a preliminary step to running shhh.seqs. Chris Quince has a series of perl scripts that fulfill a similar role [1]. This command will allow you to partition your flowgram data by sample based on the barcode, trim the flows to a specified length range, and cull sequences that are too short or have too many mismatches to barcodes and primers. + +.. _trim.flows: http://www.mothur.org/wiki/Trim.flows + + + + diff -r ee59e5cff3ba -r a6189f58fedb mothur/tools/mothur/unifrac.weighted.xml --- a/mothur/tools/mothur/unifrac.weighted.xml Wed Oct 05 10:37:11 2011 -0500 +++ b/mothur/tools/mothur/unifrac.weighted.xml Tue Nov 08 11:45:32 2011 -0600 @@ -23,7 +23,7 @@ --distance=$distance #end if $root - --processors=2 + --processors=8