# HG changeset patch # User jjohnson # Date 1307482535 14400 # Node ID fcc0778f698750df4340d4e612ad84d4af554b30 # Parent 3202a38e44d94a74e711831d24362391e4fa7814 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository diff -r 3202a38e44d9 -r fcc0778f6987 mothur/README --- a/mothur/README Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/README Tue Jun 07 17:35:35 2011 -0400 @@ -1,6 +1,6 @@ Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page -Install mothur v.1.15.0 on your galaxy system so galaxy can execute the mothur command +Install mothur v.1.16.0 on your galaxy system so galaxy can execute the mothur command http://www.mothur.org/wiki/Download_mothur http://www.mothur.org/wiki/Installation ( This Galaxy iMothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode ) @@ -132,7 +132,12 @@ + + + + + @@ -146,38 +151,40 @@ - + + + + + + + + + + + + - - - - - + - - - - - - - - - - + + + + + @@ -199,6 +206,8 @@ + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/lib/galaxy/datatypes/metagenomics.py --- a/mothur/lib/galaxy/datatypes/metagenomics.py Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/lib/galaxy/datatypes/metagenomics.py Tue Jun 07 17:35:35 2011 -0400 @@ -484,33 +484,29 @@ fh.close() return False -class Alignment(Tabular): - file_ext = 'align' - def __init__(self, **kwd): - """Initialize secondary structure map datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] - class AlignCheck(Tabular): file_ext = 'align.check' def __init__(self, **kwd): """Initialize secondary structure map datatype""" Tabular.__init__( self, **kwd ) self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] + self.columns = 8 class Names(Tabular): file_ext = 'names' def __init__(self, **kwd): - """Name file shows the relationship between a representative sequence(col 1) and the sequences it represents(col 2)""" + """Name file shows the relationship between a representative sequence(col 1) and the sequences(comma-separated) it represents(col 2)""" Tabular.__init__( self, **kwd ) self.column_names = ['name','representatives'] + self.columns = 2 class Summary(Tabular): file_ext = 'summary' def __init__(self, **kwd): - """Name file shows the relationship between a representative sequence(col 1) and the sequences it represents(col 2)""" + """summarizes the quality of sequences in an unaligned or aligned fasta-formatted sequence file""" Tabular.__init__( self, **kwd ) self.column_names = ['seqname','start','end','nbases','ambigs','polymer'] + self.columns = 6 class Group(Tabular): file_ext = 'groups' @@ -518,6 +514,15 @@ """Name file shows the relationship between a representative sequence(col 1) and the sequences it represents(col 2)""" Tabular.__init__( self, **kwd ) self.column_names = ['name','group'] + self.columns = 2 + +class Design(Tabular): + file_ext = 'design' + def __init__(self, **kwd): + """Name file shows the relationship between a group(col 1) and a grouping (col 2), providing a way to merge groups.""" + Tabular.__init__( self, **kwd ) + self.column_names = ['group','grouping'] + self.columns = 2 class AccNos(Tabular): file_ext = 'accnos' @@ -525,6 +530,7 @@ """A list of names""" Tabular.__init__( self, **kwd ) self.column_names = ['name'] + self.columns = 1 class Oligos( data.Text ): file_ext = 'oligos' @@ -781,6 +787,62 @@ return False +class Axes(Tabular): + file_ext = 'axes' + + def __init__(self, **kwd): + """Initialize axes datatype""" + Tabular.__init__( self, **kwd ) + def sniff( self, filename ): + """ + Determines whether the file is an axes format + The first line may have column headings. + The following lines have the name in the first column plus float columns for each axis. + ==> 98_sq_phylip_amazon.fn.unique.pca.axes <== + group axis1 axis2 + forest 0.000000 0.145743 + pasture 0.145743 0.000000 + + ==> 98_sq_phylip_amazon.nmds.axes <== + axis1 axis2 + U68589 0.262608 -0.077498 + U68590 0.027118 0.195197 + U68591 0.329854 0.014395 + """ + try: + fh = open( filename ) + count = 0 + line = fh.readline() + line = line.strip() + col_cnt = None + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + if line: + fields = line.split('\t') + if col_cnt == None: # ignore values in first line as they may be column headings + col_cnt = len(fields) + else: + if len(fields) != col_cnt : + return False + try: + for i in range(1, col_cnt): + check = float(fields[i]) + except ValueError: + return False + count += 1 + if count > 10: + return True + if count > 0: + return True + except: + pass + finally: + fh.close() + return False + ## Qiime Classes class MetadataMapping(Tabular): diff -r 3202a38e44d9 -r fcc0778f6987 mothur/suite_config.xml --- a/mothur/suite_config.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/suite_config.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,210 +1,240 @@ - + Mothur metagenomics commands as Galaxy tools - + Calculate the number of potentially misaligned bases - + Align sequences to a template alignment - + Order Sequences by OTU - + + Generate a newick trees for dissimilarity among groups + + Find putative chimeras using bellerophon - + Find putative chimeras using ccode - + Find putative chimeras using chimeraCheck - + Find putative chimeras using pintail - + Find putative chimeras using slayer - + Trim sequences to a specified length - + Assign sequences to taxonomy - + Assign sequences to taxonomy - + Generate a tree using relaxed neighbor joining - + Assign sequences to OTUs (Dotur implementation) - + Group sequences that are part of a larger sequence - + + Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices + + Assign sequences to OTUs (Operational Taxonomic Unit) - + Generate collector's curves for calculators on OTUs - + Summary of calculator values for OTUs - + Find a consensus sequence for each OTU or phylotype - + + correlation of data to axes + + Remove gap characters from sequences - + Return all sequences - + calculate uncorrected pairwise distances between aligned sequences - + Generate a phylip-formatted dissimilarity distance matrix among multiple groups - + Convert fastq to fasta and quality - + removes columns from alignments - + Select groups - + + group names from shared or from list and group + + Picks by taxon - + Generate a fasta with a representative sequence for each OTU - + Get otus containing sequences from specified groups - + Calculate the relative abundance of each otu - + Picks sequences by name - + Assign sequences to OTUs (Operational Taxonomic Unit) - + Generate a heatmap for OTUs - + Generate a heatmap for pariwise similarity - + Identify indicator "species" for nodes on a tree - + Cramer-von Mises tests communities for the same structure - + Lists the names of the sequences - + + Assign groups to Sets + + Make a group file - + Merge data - + + Merge groups in a shared file + + + generate principle components plot data + + + generate non-metric multidimensional scaling data + + Normalize the number of sequences per group to a specified level - + calculate uncorrected pairwise distances between sequences - + Order Sequences by OTU - + Describes whether two or more communities have the same structure - + + generate principle components plot data + + Principal Coordinate Analysis - + Alpha Diversity calculate unique branch length - + Assign sequences to OTUs based on taxonomy - + Remove sequences due to pyrosequencing errors - + Generate inter-sample rarefaction curves for OTUs - + Generate intra-sample rarefaction curves for OTUs - + Read OTU list and group to create a shared file - + Remove groups - + Picks by taxon - + Remove otus containing sequences from specified groups - + + Remove rare OTUs + + Remove sequences by name - + Reverse complement the sequences - + Screen sequences - + Summarize the quality of sequences - + Separate sequences into rare and abundant groups - + Generates a fasta file for each group - + Create a sub sample - + Summarize the quality of sequences - - Summary of calculator values for OTUs - - + Summary of calculator values for OTUs - - Generate a newick tree for dissimilarity among groups - - - Trim sequences - primers, barcodes, quality - - - Describes whether two or more communities have the same structure + + Summary of calculator values for OTUs - - Describes whether two or more communities have the same structure - - - Return unique sequences - - - Generate Venn diagrams gor groups + + Generate a newick tree for dissimilarity among groups Draw a Phylogenic Tree + + Trim sequences - primers, barcodes, quality + + + Describes whether two or more communities have the same structure + + + Describes whether two or more communities have the same structure + + + Return unique sequences + + + Generate Venn diagrams gor groups + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tool-data/mothur_calculators.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tool-data/mothur_calculators.loc Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,91 @@ +#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): +# +## +# 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 diversity +bergerparker single xxxx Community diversity the Berger-Parker index +coverage single sing Community diversity the sampling coverage 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 +simpsoneven single sing Community diversity the Simpson index +smithwilson single sing Smith and Wilson's metric of community evenness +##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 +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 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/align.check.xml --- a/mothur/tools/mothur/align.check.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/align.check.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Calculate the number of potentially misaligned bases mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/align.seqs.xml --- a/mothur/tools/mothur/align.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/align.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Align sequences to a template alignment mothur_wrapper.py @@ -23,6 +23,7 @@ --flip=true --threshold=$reverse.threshold #end if + --processors=2 @@ -50,7 +51,9 @@ - + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/bin.seqs.xml --- a/mothur/tools/mothur/bin.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/bin.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Order Sequences by OTU mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/bootstrap.shared.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/bootstrap.shared.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,126 @@ + + Generate a newick trees for dissimilarity among groups + + #* +98_sq_phylip_amazon.fn.jclass.bootunique.tre +98_sq_phylip_amazon.fn.thetayc.bootunique.tre +98_sq_phylip_amazon.fn.jclass.bootunique.cons.pairs +98_sq_phylip_amazon.fn.jclass.bootunique.cons.tre +98_sq_phylip_amazon.fn.thetayc.bootunique.cons.pairs +98_sq_phylip_amazon.fn.thetayc.bootunique.cons.tre +98_sq_phylip_amazon.fn.jclass.boot0.00.tre +98_sq_phylip_amazon.fn.thetayc.boot0.00.tre +98_sq_phylip_amazon.fn.jclass.boot0.00.cons.pairs +98_sq_phylip_amazon.fn.jclass.boot0.00.cons.tre +98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.pairs +98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.tre + *# + mothur_wrapper.py + --cmd='bootstrap.shared' + --result='^mothur.\S+\.logfile$:'$logfile + --outputdir='$logfile.extra_files_path' + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.tre)$:tre','^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.cons\.tre)$:tre','^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.cons\.pairs)$:txt' + --READ_cmd='read.otu' + #if $input.source == 'similarity': + --READ_list=$input.otu + #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: + --READ_group='$otu_group' + #end if + #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: + --READ_label='$input.label' + #end if + #elif $input.source == 'shared': + --READ_shared=$input.otu + #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: + --READ_label='$input.label' + #end if + #end if + #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: + --groups=$input.groups + #end if + #if $calc.__str__ != "None" and len($calc.__str__) > 0: + --calc=$calc + #end if + #if int($iters.__str__) > 0: + --iters=$iters + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mothur + + + + +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The bootstrap.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. + +.. _bootstrap.shared: http://www.mothur.org/wiki/Bootstrap.shared + + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/chimera.bellerophon.xml --- a/mothur/tools/mothur/chimera.bellerophon.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/chimera.bellerophon.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using bellerophon mothur_wrapper.py @@ -14,6 +14,7 @@ #if int($increment.__str__) > 0: --increment=$increment #end if + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/chimera.ccode.xml --- a/mothur/tools/mothur/chimera.ccode.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/chimera.ccode.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using ccode mothur_wrapper.py @@ -19,6 +19,7 @@ #if int($numwanted.__str__) > 0: --numwanted=$numwanted #end if + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/chimera.check.xml --- a/mothur/tools/mothur/chimera.check.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/chimera.check.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using chimeraCheck mothur_wrapper.py @@ -21,6 +21,7 @@ --name='$name' #end if #end if + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/chimera.pintail.xml --- a/mothur/tools/mothur/chimera.pintail.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/chimera.pintail.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using pintail mothur_wrapper.py @@ -33,6 +33,7 @@ --increment=$increment #end if --result=#echo ','.join($results) + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/chimera.slayer.xml --- a/mothur/tools/mothur/chimera.slayer.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/chimera.slayer.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using slayer mothur_wrapper.py @@ -7,7 +7,14 @@ --outputdir='$logfile.extra_files_path' --tmpdir='${logfile.extra_files_path}/input' --fasta=$fasta - --template=$alignment.template + #if $alignment.source == 'self': + --template='self' + #if $alignment.name.__str__ != "None" and len($alignment.name.__str__) > 0: + --name=$alignment.name + #end if + #else: + --template=$alignment.template + #end if #if $options.setby == 'user': --search=$options.search --window=$options.window @@ -22,7 +29,9 @@ --minbs=$options.minbs --minsnp=$options.minsnp --divergence=$options.divergence + $options.trim #end if + --processors=2 @@ -30,6 +39,7 @@ + @@ -42,6 +52,9 @@ + + + @@ -67,6 +80,7 @@ + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/chop.seqs.xml --- a/mothur/tools/mothur/chop.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/chop.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Trim sequences to a specified length mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/classify.otu.xml --- a/mothur/tools/mothur/classify.otu.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/classify.otu.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to taxonomy mothur_wrapper.py @@ -9,6 +9,9 @@ --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy' --list=$otu --taxonomy=$tax.taxonomy + #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0: + --reftaxonomy=$reftax.taxonomy + #end if #if 100 >= int($cutoff.__str__) > 0: --cutoff=$cutoff #end if @@ -36,13 +39,34 @@ + + + + + + + + + + + + + + + + + + + - + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/classify.seqs.xml --- a/mothur/tools/mothur/classify.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/classify.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to taxonomy mothur_wrapper.py @@ -38,6 +38,7 @@ --search=$classify.search.algorithm #end if #end if + --processors=2 @@ -81,9 +82,13 @@ - + + + - + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/clearcut.xml --- a/mothur/tools/mothur/clearcut.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/clearcut.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generate a tree using relaxed neighbor joining mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/cluster.classic.xml --- a/mothur/tools/mothur/cluster.classic.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/cluster.classic.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Dotur implementation) mothur_wrapper.py @@ -68,8 +68,8 @@ - - + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/cluster.fragments.xml --- a/mothur/tools/mothur/cluster.fragments.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/cluster.fragments.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Group sequences that are part of a larger sequence mothur_wrapper.py @@ -7,10 +7,21 @@ --outputdir='$logfile.extra_files_path' --fasta=$fasta --name=$names + #if int($diffs.__str__) > 0: + --diffs=$diffs + #end if + #if 100 >= int($percent.__str__) > 0: + --percent=$percent + #end if + + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/cluster.split.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/cluster.split.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,136 @@ + + Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices + + mothur_wrapper.py + --cmd='cluster.split' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist + --outputdir='$logfile.extra_files_path' + #if $splitby.splitmethod == "distance": + #if $splitby.matrix.format == "column": + --column=$splitby.matrix.dist + --name=$splitby.matrix.name + #elif $splitby.matrix.format == "phylip": + --phylip=$splitby.matrix.dist + #if $splitby.matrix.name.__str__ != "None" and len($splitby.matrix.name.__str__) > 0: + --name=$splitby.matrix.name + #end if + #end if + --splitmethod=$splitby.splitmethod + #elif $splitby.splitmethod == "classify": + --column=$splitby.dist + --name=$splitby.name + --taxonomy=$splitby.taxonomy + #if $splitby.taxlevel > 1: + --taxlevel=$splitby.taxlevel + #end if + --splitmethod=$splitby.splitmethod + #elif $splitby.splitmethod == "fasta": + --fasta=$splitby.fasta + --name=$splitby.name + --taxonomy=$splitby.taxonomy + #if $splitby.taxlevel > 1: + --taxlevel=$splitby.taxlevel + #end if + --splitmethod=$splitby.splitmethod + #end if + #if len($method.__str__) > 0: + --method=$method + #end if + #if float($cutoff.__str__) > 0.0: + --cutoff=$cutoff + #end if + $hard + #if len($precision.__str__) > 0: + --precision=$precision + #end if + $large + --processors=1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 cluster.split_ command assign sequences to OTUs (Operational Taxonomy Unit). + +.. _cluster.split: http://www.mothur.org/wiki/Cluster.split + + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/cluster.xml --- a/mothur/tools/mothur/cluster.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/cluster.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Operational Taxonomic Unit) mothur_wrapper.py @@ -68,8 +68,8 @@ - - + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/collect.shared.xml --- a/mothur/tools/mothur/collect.shared.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/collect.shared.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generate collector's curves for calculators on OTUs mothur_wrapper.py @@ -62,6 +62,7 @@ + @@ -74,7 +75,7 @@ - + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/collect.single.xml --- a/mothur/tools/mothur/collect.single.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/collect.single.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Summary of calculator values for OTUs mothur_wrapper.py @@ -35,10 +35,11 @@ + - + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/consensus.seqs.xml --- a/mothur/tools/mothur/consensus.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/consensus.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Find a consensus sequence for each OTU or phylotype mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/corr.axes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/corr.axes.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,93 @@ + + correlation of data to axes + + mothur_wrapper.py + ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list + #import re, os.path + --cmd='corr.axes' + --outputdir='$logfile.extra_files_path' + #if $input.source == 'shared': + #if isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): + --shared=$input.otu + #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__): + --relabund=$input.otu + #end if + #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: + --label=$input.label + #end if + #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: + --groups=$input.groups + #end if + #else: + --metadata=$input.metadata + #end if + --method=$method + --axes=$axes + #if int($numaxes.__str__) > 0: + --numaxes=$numaxes + #end if + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.corr.axes$:'$corr_axes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 corr.axes_ command calculates the correlation of data to axes. + +.. _corr.axes: http://www.mothur.org/wiki/Corr.axes + + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/degap.seqs.xml --- a/mothur/tools/mothur/degap.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/degap.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Remove gap characters from sequences mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/deunique.seqs.xml --- a/mothur/tools/mothur/deunique.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/deunique.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Return all sequences mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/dist.seqs.xml --- a/mothur/tools/mothur/dist.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/dist.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + calculate uncorrected pairwise distances between aligned sequences mothur_wrapper.py @@ -16,6 +16,7 @@ #if len($output.__str__) > 0: --output=$output #end if + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/dist.shared.xml --- a/mothur/tools/mothur/dist.shared.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/dist.shared.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generate a phylip-formatted dissimilarity distance matrix among multiple groups mothur_wrapper.py @@ -30,6 +30,9 @@ --READ_label='$input.label' #end if #end if + #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: + --groups=$input.groups + #end if #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc=$calc #end if @@ -81,7 +84,7 @@ - + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/fastq.info.xml --- a/mothur/tools/mothur/fastq.info.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/fastq.info.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Convert fastq to fasta and quality mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/filter.seqs.xml --- a/mothur/tools/mothur/filter.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/filter.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + removes columns from alignments mothur_wrapper.py @@ -30,6 +30,7 @@ #if $hard.__str__ != "None" and len($hard.__str__) > 0: --hard=$hard #end if + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/get.group.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/get.group.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,78 @@ + + group names from shared or from list and group + + mothur_wrapper.py + --cmd='get.group' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.bootGroups$:'$bootgroups + --outputdir='$logfile.extra_files_path' + --READ_cmd='read.otu' + #if $input.source == 'similarity': + --READ_list=$input.otu + #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: + --READ_group='$otu_group' + #end if + #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: + --READ_groups='$input.groups' + #end if + #elif $input.source == 'shared': + --READ_shared=$input.otu + #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: + --READ_group='$otu_group' + #end if + #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 get.group_ command generate principle components plot data. + +.. _get.group: http://www.mothur.org/wiki/Get.group + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/get.groups.xml --- a/mothur/tools/mothur/get.groups.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/get.groups.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Select groups mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/get.lineage.xml --- a/mothur/tools/mothur/get.lineage.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/get.lineage.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Picks by taxon mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/get.oturep.xml --- a/mothur/tools/mothur/get.oturep.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/get.oturep.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generate a fasta with a representative sequence for each OTU mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/get.otus.xml --- a/mothur/tools/mothur/get.otus.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/get.otus.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Get otus containing sequences from specified groups mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/get.relabund.xml --- a/mothur/tools/mothur/get.relabund.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/get.relabund.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Calculate the relative abundance of each otu mothur_wrapper.py @@ -20,6 +20,9 @@ --READ_label='$input.label' #end if #end if + #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: + --groups=$input.groups + #end if #if $scale.__str__ != "None" and len($scale.__str__) > 0: --scale=$scale #end if @@ -53,6 +56,7 @@ + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/get.seqs.xml --- a/mothur/tools/mothur/get.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/get.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Picks sequences by name mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/hcluster.xml --- a/mothur/tools/mothur/hcluster.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/hcluster.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Operational Taxonomic Unit) mothur_wrapper.py @@ -71,8 +71,8 @@ - - + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/heatmap.bin.xml --- a/mothur/tools/mothur/heatmap.bin.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/heatmap.bin.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generate a heatmap for OTUs mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/heatmap.sim.xml --- a/mothur/tools/mothur/heatmap.sim.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/heatmap.sim.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generate a heatmap for pariwise similarity mothur_wrapper.py @@ -70,7 +70,7 @@ - + @@ -84,6 +84,7 @@ + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/indicator.xml --- a/mothur/tools/mothur/indicator.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/indicator.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Identify indicator "species" for nodes on a tree mothur_wrapper.py @@ -18,6 +18,9 @@ #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if + #if $design.__str__ != "None" and len($design.__str__) > 0: + --design=$design + #end if --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.indicator.tre$:'$tree_out,'^\S+\.indicator.summary$:'$summary @@ -37,6 +40,8 @@ + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/libshuff.xml --- a/mothur/tools/mothur/libshuff.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/libshuff.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Cramer-von Mises tests communities for the same structure mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/list.seqs.xml --- a/mothur/tools/mothur/list.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/list.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Lists the names of the sequences mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/make.design.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/make.design.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,57 @@ + + Assign groups to Sets + cat $generated_design > $design + + + + + + + + + + + + + + + + +#for $grouping in $groupings: +#set grp_str = $grouping.groups.__str__ +#if grp_str != None and len(grp_str) > 0: +#for $grp in grp_str.split(','): +$grp $grouping.name +#end for +#end if +#end for + + + + + + + mothur + + + + +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +Make Design creates a design file for use in mothur commands: merge.groups_, indicator_, and metastats_. +A design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to. + +.. _merge.groups: http://www.mothur.org/wiki/Merge.groups +.. _indicator: http://www.mothur.org/wiki/Indicator +.. _metastats: http://www.mothur.org/wiki/Metastats + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/make.group.xml --- a/mothur/tools/mothur/make.group.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/make.group.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Make a group file mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/merge.files.xml --- a/mothur/tools/mothur/merge.files.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/merge.files.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,22 +1,57 @@ - + Merge data mothur_wrapper.py --cmd='merge.files' --result='^mothur.\S+\.logfile$:'$logfile,'mergefile:'$output --outputdir='$logfile.extra_files_path' - --input=${input}#for i in $inputs#,${i.input}#end for# + --input=${merge.input}#for i in $merge.inputs#,${i.input}#end for# --output='mergefile' - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + mothur diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/merge.groups.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/merge.groups.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,100 @@ + + Merge groups in a shared file + + mothur_wrapper.py + --cmd='merge.groups' + ## 98_sq_phylip_amazon.fn.merge.shared + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.merge\.\S+$:'$shared + --outputdir='$logfile.extra_files_path' + --shared=$otu + #if $design.source == 'hist': + --design=$design_dataset + #else: + --design=$generated_design + #end if + #if $groups.__str__ != "None" and len($groups.__str__) > 0: + --groups=$groups + #end if + #if $label.__str__ != "None" and len($label.__str__) > 0: + --label='$label' + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +#if $design.source == 'build': +#for $grouping in $design.groupings: +#set grp_str = $grouping.groups.__str__ +#if grp_str != None and len(grp_str) > 0: +#for $grp in grp_str.split(','): +$grp $grouping.name +#end for +#end if +#end for +#end if + + + + + + + + mothur + + + + +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The merge.groups_ command reads a shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file. + +.. _merge.groups: http://www.mothur.org/wiki/Merge.groups + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/metastats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/metastats.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,121 @@ + + generate principle components plot data + + mothur_wrapper.py + --cmd='metastats' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.metastats$:'$metastats + --outputdir='$logfile.extra_files_path' + --READ_cmd='read.otu' + #if $input.source == 'similarity': + --READ_list=$input.otu + #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: + --READ_group='$otu_group' + #end if + #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: + --READ_groups='$input.groups' + #end if + #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: + --READ_label='$input.label' + #end if + #elif $input.source == 'shared': + --READ_shared=$input.otu + #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: + --READ_label='$input.label' + #end if + #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: + --READ_groups='$input.groups' + #end if + #end if + #if int($iters.__str__) > 0: + --iters=$iters + #end if + #if 1 >= $threshold >= 0: + --threshold=$threshold + #end if + #if $design.__str__ != "None" and len($design.__str__) > 0: + --design=$design + #if $sets.__str__ != "None" and len($sets.__str__) > 0: + --sets=$sets + #end if + #end if + --processors=2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mothur + + + + +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The metastats_ command generate principle components plot data. + +.. _metastats: http://www.mothur.org/wiki/Metastats + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/mothur_wrapper.py --- a/mothur/tools/mothur/mothur_wrapper.py Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/mothur_wrapper.py Tue Jun 07 17:35:35 2011 -0400 @@ -46,6 +46,7 @@ debug = False #debug = True +max_processors = 1 def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) @@ -80,6 +81,10 @@ pass html.write('\n\n\n') html.close() + #Overide the processors option + def processors_callback(option, opt, value, parser): + val = value if value <= max_processors else max_processors + setattr(parser.values, option.dest, val) #Strip out "(xx)" confidence values from a taxonomy list def remove_confidence_callback(option, opt, value, parser): # val = "'" + re.sub('$\d+$','',value) + "'" @@ -162,6 +167,7 @@ cmd_dict = dict() cmd_dict['merge.files'] = dict({'required' : ['input','output']}) cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : ['output']}) + cmd_dict['merge.groups'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label']}) cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'outputs' : ['.names']}) cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']}) @@ -169,54 +175,60 @@ cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['names']}) cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','names'], 'optional' : []}) cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['keep','short']}) - cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard']}) - cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport']}) - cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['group','oligos','qfile','qaverage','qthreshold','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles']}) + cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']}) + cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']}) + cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['group','oligos','qfile','qaverage','qthreshold','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']}) cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]}) cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) - cmd_dict['align.seqs'] = dict({'required' : ['candidate','template'], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold']}) + cmd_dict['align.seqs'] = dict({'required' : ['candidate','template'], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']}) cmd_dict['align.check'] = dict({'required' : ['fasta','map']}) cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['names','diffs']}) cmd_dict['bin.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','label','group']}) - cmd_dict['classify.seqs'] = dict({'required' : ['fasta','template','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs']}) - cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','probs']}) + cmd_dict['classify.seqs'] = dict({'required' : ['fasta','template','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']}) + cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']}) # label=0.01-0.02-0.03 from 0.01,0.02,0.03 string.replace(options.label,',','-') - cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment']}) - cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','template'], 'optional' : ['filter','mask','window','numwanted']}) - cmd_dict['chimera.check'] = dict({'required' : ['fasta','template'], 'optional' : ['ksize','svg','name','increment']}) - cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','template'], 'optional' : ['conservation','quantile','filter','mask','window','increment']}) - cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','template'], 'optional' : ['search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign']}) - cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff']}) - cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend']}) + cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']}) + cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','template'], 'optional' : ['filter','mask','window','numwanted','processors']}) + cmd_dict['chimera.check'] = dict({'required' : ['fasta','template'], 'optional' : ['ksize','svg','name','increment','processors']}) + cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','template'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']}) + cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','template'], 'optional' : ['name','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','processors']}) + cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','processors']}) + cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']}) cmd_dict['read.dist'] = dict({'required' : [['phylip','column']], 'optional' : ['name','cutoff','hard','precision','sim','group']}) cmd_dict['read.otu'] = dict({'required' : [['rabund','sabund','list','shared','relabund']], 'optional' : ['label','group','groups','ordergroup']}) cmd_dict['read.tree'] = dict({'required' : ['tree'], 'optional' : ['name','group']}) cmd_dict['cluster'] = dict({'required' : [] , 'optional' : ['method','cutoff','hard','precision']}) cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund']}) - cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name']}) - cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode']}) + cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']}) + cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']}) + cmd_dict['metastats'] = dict({'required' : ['design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']}) + cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode','processors']}) cmd_dict['summary.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','all','distance']}) cmd_dict['collect.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','freq']}) cmd_dict['collect.shared'] = dict({'required' : [], 'optional' : ['calc','label','freq','groups','all']}) - cmd_dict['rarefaction.single'] = dict({'required' : [], 'optional' : ['calc','abund','iters','label','freq']}) + cmd_dict['rarefaction.single'] = dict({'required' : [], 'optional' : ['calc','abund','iters','label','freq','processors']}) cmd_dict['rarefaction.shared'] = dict({'required' : [], 'optional' : ['label','iters','groups','jumble']}) cmd_dict['normalize.shared'] = dict({'required' : [], 'optional' : ['label','method','norm','groups']}) cmd_dict['dist.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','output']}) cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']}) cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : []}) cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']}) - cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random']}) - cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random']}) - cmd_dict['parsimony'] = dict({'required' : [], 'optional' : ['groups','iters','random']}) + cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','processors']}) + cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','processors']}) + cmd_dict['parsimony'] = dict({'required' : [], 'optional' : ['groups','iters','random','processors']}) cmd_dict['sffinfo'] = dict({'required' : ['sff'], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']}) cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []}) cmd_dict['heatmap.bin'] = dict({'required' : [], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']}) cmd_dict['heatmap.sim'] = dict({'required' : [], 'optional' : ['calc','phylip','column','name','label','groups']}) cmd_dict['venn'] = dict({'required' : [], 'optional' : ['calc','label','groups','nseqs','permute']}) cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : []}) + cmd_dict['pca'] = dict({'required' : [], 'optional' : ['label','groups','metric']}) + cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']}) + cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']}) + cmd_dict['get.group'] = dict({'required' : [], 'optional' : []}) cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']}) - cmd_dict['phylo.diversity'] = dict({'required' : [],'optional' : ['groups','iters','freq','processors','scale','rarefy','collect','summary']}) + cmd_dict['phylo.diversity'] = dict({'required' : [],'optional' : ['groups','iters','freq','processors','scale','rarefy','collect','summary','processors']}) cmd_dict['get.oturep'] = dict({'required' : ['fasta','list'], 'optional' : ['phylip','column','name','label','group','groups','sorted','precision','cutoff','large','weighted']}) cmd_dict['get.relabund'] = dict({'required' : [],'optional' : ['scale','label','groups']}) cmd_dict['libshuff'] = dict({'required' : [],'optional' : ['iters','form','step','cutoff']}) @@ -233,11 +245,12 @@ cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) + cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']}) cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']}) - cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size']}) + cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']}) cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label']}) - cmd_dict['indicator'] = dict({'required' : ['tree',['shared','relabund']], 'optional' : ['groups','label']}) + cmd_dict['indicator'] = dict({'required' : ['tree',['shared','relabund']], 'optional' : ['groups','label','design']}) parser = optparse.OptionParser() # Options for managing galaxy interaction parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' ) @@ -299,7 +312,9 @@ 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( '--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' ) + parser.add_option( '--taxlevel', dest='taxlevel', type="int", help='A Taxonomy level' ) # parser.add_option( '--taxon', dest='taxon', action="callback", callback=remove_confidence_callback, help='A Taxon' ) parser.add_option( '--candidate', dest='candidate', help=' file ' ) parser.add_option( '--template', dest='template', help=' file ' ) @@ -312,6 +327,7 @@ parser.add_option( '--mismatch', dest='mismatch', type="float", help='Penalty for a mismatch, default is -1.0' ) parser.add_option( '--gapopen', dest='gapopen', type="float", help='Penalty for a opening, default is -2.0' ) parser.add_option( '--gapextend', dest='gapextend', type="float", help='Penalty for extending a gap, default is -1.0' ) + parser.add_option( '--precision', dest='precision', type="int", help='' ) parser.add_option( '--threshold', dest='threshold', type="float", help='Cutoff at which an alignment is deemed bad and the reverse complement may be tried, 0.0 - 1.0 default 0.50' ) parser.add_option( '--map', dest='map', help='File containing the secondary structure map.' ) parser.add_option( '--label', dest='label', type='string', action="callback", callback=multi_val_callback, help='Distance levels you would like a output files created for(separated by commas or dashes)' ) @@ -336,12 +352,14 @@ parser.add_option( '--countgaps', dest='countgaps', help='count gaps as bases' ) parser.add_option( '--output', dest='output', help='Format for output' ) parser.add_option( '--method', dest='method', help='Method to use for analysis - cluster' ) + parser.add_option( '--splitmethod', dest='splitmethod', help='Method to split a distance file - cluster.split' ) parser.add_option( '--abund', dest='abund', type='int', help='Threshold for rare to Abundant OTU classification' ) parser.add_option( '--size', dest='size', type='int', help='Size - sample size' ) parser.add_option( '--groupmode', dest='groupmode', help='Collate groups into one result table' ) 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( '--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' ) parser.add_option( '--quantile', dest='quantile', help='Template quantile information' ) @@ -350,6 +368,9 @@ parser.add_option( '--mincov', dest='mincov', type='int', help='Minimum coverage (0-100 percent)' ) parser.add_option( '--minbs', dest='minbs', type='int', help='Minimum bootstrap support (0-100 percent)' ) parser.add_option( '--minsnp', dest='minsnp', type='int', help='Minimum SNPs to sample(0-100 percent)' ) + parser.add_option( '--mindim', dest='mindim', type='int', help='Minimum dimensions' ) + parser.add_option( '--maxdim', dest='maxdim', type='int', help='Maximum dimensions' ) + parser.add_option( '--percent', dest='percent', type='int', help='(0-100 percent)' ) parser.add_option( '--divergence', dest='divergence', type='float', help='Divergence cutoff for chimera determination' ) parser.add_option( '--sff', dest='sff', help='Sff file' ) parser.add_option( '--sfftxt', dest='sfftxt', help='Generate a sff.txt file' ) @@ -381,6 +402,21 @@ parser.add_option( '--kimura', dest='kimura', help='' ) parser.add_option( '--jukes', dest='jukes', help='' ) parser.add_option( '--matrixout', dest='matrixout', help='' ) + parser.add_option( '--nseqs', dest='nseqs', help='' ) + parser.add_option( '--bygroup', dest='bygroup', help='' ) + parser.add_option( '--design', dest='design', help='' ) + parser.add_option( '--sets', dest='sets', help='' ) + parser.add_option( '--metric', dest='metric', help='' ) + parser.add_option( '--epsilon', dest='epsilon', help='' ) + parser.add_option( '--axes', dest='axes', help='table of name column followed by columns of axis values' ) + parser.add_option( '--numaxes', dest='numaxes', help='the number of axes' ) + parser.add_option( '--metadata', dest='metadata', help='data table with columns of floating-point values' ) + parser.add_option( '--basis', dest='basis', help='what the summary file represents' ) + parser.add_option( '--keepfirst', dest='keepfirst', help='trimming' ) + parser.add_option( '--removelast', dest='removelast', help='trimming' ) + parser.add_option( '--persample', dest='persample', help='sub sample option' ) + parser.add_option( '--timing', dest='timing', help='timing option' ) + parser.add_option( '--processors', dest='processors', type='int', action='callback', callback=processors_callback, help='Number of processors to use' ) # include read.otu options parser.add_option( '--rabund', dest='rabund', help='' ) parser.add_option( '--sabund', dest='sabund', help='' ) diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/nmds.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/nmds.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,65 @@ + + generate non-metric multidimensional scaling data + + mothur_wrapper.py + --cmd='nmds' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.nmds\.axes$:'$nmds_axes,'^\S+\.nmds\.iters$:'$nmds_iters,'^\S+\.stress\.nmds$:'$stress_nmds + --outputdir='$logfile.extra_files_path' + --phylip=$dist + #if $axes.__str__ != "None" and len($axes.__str__) > 0: + --axes=$axes + #end if + #if int($mindim.__str__) > 0: + --mindim=$mindim + #end if + #if int($maxdim.__str__) >= int($mindim.__str__): + --maxdim=$maxdim + #end if + #if int($iters.__str__) > 0: + --iters=$iters + #end if + #if int($maxiters.__str__) > 0: + --maxiters=$maxiters + #end if + #if float($epsilon.__str__) > 0.0: + --epsilon=$epsilon + #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 nmds_ command generates non-metric multidimensional scaling data + +.. _nmds: http://www.mothur.org/wiki/Nmds + + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/normalize.shared.xml --- a/mothur/tools/mothur/normalize.shared.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/normalize.shared.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Normalize the number of sequences per group to a specified level mothur_wrapper.py @@ -59,6 +59,7 @@ + @@ -75,6 +76,7 @@ + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/pairwise.seqs.xml --- a/mothur/tools/mothur/pairwise.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/pairwise.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + calculate uncorrected pairwise distances between sequences mothur_wrapper.py @@ -21,6 +21,7 @@ #if len($output.__str__) > 0: --output=$output #end if + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/parse.list.xml --- a/mothur/tools/mothur/parse.list.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/parse.list.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Order Sequences by OTU mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/parsimony.xml --- a/mothur/tools/mothur/parsimony.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/parsimony.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Describes whether two or more communities have the same structure mothur_wrapper.py @@ -16,6 +16,7 @@ #if int($iters.__str__) > 0: --iters=$iters #end if + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/pca.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/pca.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,102 @@ + + generate principle components plot data + + mothur_wrapper.py + ## 98_sq_phylip_amazon.fn.unique.pca.axes + ## 98_sq_phylip_amazon.fn.unique.pca.loadings + --cmd='pca' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pca.axes$:'$pca_axes,'^\S+\.pca.loadings$:'$pca_loadings + --outputdir='$logfile.extra_files_path' + --READ_cmd='read.otu' + #if $input.source == 'similarity': + --READ_list=$input.otu + #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: + --READ_group='$otu_group' + #end if + #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: + --READ_groups='$input.groups' + #end if + #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: + --READ_label='$input.label' + #end if + #elif $input.source == 'shared': + --READ_shared=$input.otu + #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: + --READ_label='$input.label' + #end if + #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: + --READ_groups='$input.groups' + #end if + #end if + $metric + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mothur + + + + +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The pca_ command generate principle components plot data. + +.. _pca: http://www.mothur.org/wiki/Pca + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/pcoa.xml --- a/mothur/tools/mothur/pcoa.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/pcoa.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,9 +1,9 @@ - + Principal Coordinate Analysis mothur_wrapper.py --cmd='pcoa' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pcoa$:'$pca,'^\S+\.pcoa.loadings$:'$loadings + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pcoa\.axes$:'$pcoa,'^\S+\.pcoa.loadings$:'$loadings --outputdir='$logfile.extra_files_path' --phylip=$phylip @@ -12,7 +12,7 @@ - + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/phylo.diversity.xml --- a/mothur/tools/mothur/phylo.diversity.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/phylo.diversity.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Alpha Diversity calculate unique branch length mothur_wrapper.py @@ -23,6 +23,7 @@ $summary $collect $rarefy + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/phylotype.xml --- a/mothur/tools/mothur/phylotype.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/phylotype.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs based on taxonomy mothur_wrapper.py @@ -32,7 +32,7 @@ - + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/pre.cluster.xml --- a/mothur/tools/mothur/pre.cluster.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/pre.cluster.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Remove sequences due to pyrosequencing errors mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/rarefaction.shared.xml --- a/mothur/tools/mothur/rarefaction.shared.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/rarefaction.shared.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generate inter-sample rarefaction curves for OTUs mothur_wrapper.py @@ -60,6 +60,7 @@ + @@ -74,7 +75,7 @@ - + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/rarefaction.single.xml --- a/mothur/tools/mothur/rarefaction.single.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/rarefaction.single.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generate intra-sample rarefaction curves for OTUs mothur_wrapper.py @@ -24,10 +24,11 @@ #if int($iters.__str__) > 0: --iters=$iters #end if - #if float($freq.__str__) > 0: --freq=$freq #end if + --processors=2 + @@ -35,10 +36,11 @@ + - + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/read.otu.xml --- a/mothur/tools/mothur/read.otu.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/read.otu.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Read OTU list and group to create a shared file mothur_wrapper.py @@ -9,7 +9,6 @@ --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund' #end if - --cmd='read.otu' --list=$otu --group=$otu_group #if $label.__str__ != "None" and len($label.__str__) > 0: diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/remove.groups.xml --- a/mothur/tools/mothur/remove.groups.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/remove.groups.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Remove groups mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/remove.lineage.xml --- a/mothur/tools/mothur/remove.lineage.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/remove.lineage.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Picks by taxon mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/remove.otus.xml --- a/mothur/tools/mothur/remove.otus.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/remove.otus.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Remove otus containing sequences from specified groups mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/remove.rare.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/remove.rare.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,93 @@ + + Remove rare OTUs + + mothur_wrapper.py + ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list + #import re, os.path + #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] + --cmd='remove.rare' + --outputdir='$logfile.extra_files_path' + #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): + --shared=$otu + #if $group_in.__str__ != "None" and len($group_in.__str__) > 0: + --group=$group_in + #end if + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_shared.__str__] + #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): + --rabund=$otu + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_rabund.__str__] + #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__): + --sabund=$otu + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_sabund.__str__] + #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): + --list=$otu + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_list.__str__] + $bygroup + #end if + #if $label.__str__ != "None" and len($label.__str__) > 0: + --label=$label + #end if + #if $groups.__str__ != "None" and len($groups.__str__) > 0: + --groups=$groups + #end if + --nseqs=$nseqs + --result=#echo ','.join($results) + + + + + + + + + + + + + + + + + + + + + + + + + otu.datatype == 'list' + + + otu.datatype == 'rabund' + + + otu.datatype == 'sabund' + + + otu.datatype == 'shared' + + + + 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 remove.rare_ command reads one of the following file types: list, rabund, sabund or shared file. It outputs a new file after removing the rare otus. + +.. _remove.rare: http://www.mothur.org/wiki/Remove.rare + + + + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/remove.seqs.xml --- a/mothur/tools/mothur/remove.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/remove.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Remove sequences by name mothur_wrapper.py @@ -41,8 +41,8 @@ - - + + @@ -53,12 +53,23 @@ - + + + fasta_in != None + + + + qfile_in != None + + + name_in != None diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/reverse.seqs.xml --- a/mothur/tools/mothur/reverse.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/reverse.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Reverse complement the sequences mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/screen.seqs.xml --- a/mothur/tools/mothur/screen.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/screen.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Screen sequences mothur_wrapper.py @@ -47,6 +47,7 @@ #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input_alignreport.__str__)) + ":'" + $output_alignreport.__str__] #end if --result=#echo ','.join($results) + --processors=2 @@ -71,19 +72,10 @@ - + - diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/sffinfo.xml --- a/mothur/tools/mothur/sffinfo.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/sffinfo.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Summarize the quality of sequences mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/split.abund.xml --- a/mothur/tools/mothur/split.abund.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/split.abund.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Separate sequences into rare and abundant groups mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/split.groups.xml --- a/mothur/tools/mothur/split.groups.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/split.groups.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generates a fasta file for each group mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/sub.sample.xml --- a/mothur/tools/mothur/sub.sample.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/sub.sample.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Create a sub sample mothur_wrapper.py @@ -20,6 +20,7 @@ #if $input.use_group.groups.__str__ != "None" and len($input.use_group.groups.__str__) > 0: --groups=$input.use_group.groups #end if + $input.use_group.persample #end if #elif $input.format == "list": --list=$input.otu_in @@ -30,6 +31,7 @@ #if $input.use_group.groups.__str__ != "None" and len($input.use_group.groups.__str__) > 0: --groups=$input.use_group.groups #end if + $input.use_group.persample #end if #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: --label=$input.label @@ -88,6 +90,7 @@ + @@ -108,6 +111,7 @@ + @@ -130,6 +134,7 @@ + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/summary.seqs.xml --- a/mothur/tools/mothur/summary.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/summary.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Summarize the quality of sequences mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/summary.shared.xml --- a/mothur/tools/mothur/summary.shared.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/summary.shared.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Summary of calculator values for OTUs mothur_wrapper.py @@ -83,7 +83,7 @@ - + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/summary.single.xml --- a/mothur/tools/mothur/summary.single.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/summary.single.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Summary of calculator values for OTUs mothur_wrapper.py @@ -25,6 +25,7 @@ --size=$size #end if $groupmode + --processors=2 @@ -36,7 +37,7 @@ - + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/tree.shared.xml --- a/mothur/tools/mothur/tree.shared.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/tree.shared.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generate a newick tree for dissimilarity among groups mothur_wrapper.py @@ -59,6 +59,7 @@ + @@ -71,7 +72,7 @@ - + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/trim.seqs.xml --- a/mothur/tools/mothur/trim.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/trim.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Trim sequences - primers, barcodes, quality mothur_wrapper.py @@ -17,6 +17,12 @@ #if $maxhomop > 0: --maxhomop=$maxhomop #end if + #if $keepfirst > 0: + --keepfirst=$keepfirst + #end if + #if $removelast > 0: + --removelast=$removelast + #end if #if $oligo.add == "yes": --oligos=$oligo.oligos #if $oligo.bdiffs > 0: @@ -48,43 +54,47 @@ + + - + - - - - + + + + - + - - - - + + + + - + - qfile != None and len(qfile) > 0 + qfile != none and len(qfile) > 0 - qfile != None and len(qfile) > 0 + qfile != none and len(qfile) > 0 @@ -94,7 +104,7 @@ -**Mothur Overview** +**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, diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/unifrac.unweighted.xml --- a/mothur/tools/mothur/unifrac.unweighted.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/unifrac.unweighted.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Describes whether two or more communities have the same structure mothur_wrapper.py @@ -23,6 +23,7 @@ #if $distance.__str__ != "false": --distance=$distance #end if + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/unifrac.weighted.xml --- a/mothur/tools/mothur/unifrac.weighted.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/unifrac.weighted.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Describes whether two or more communities have the same structure mothur_wrapper.py @@ -23,6 +23,7 @@ #if $distance.__str__ != "false": --distance=$distance #end if + --processors=2 diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/unique.seqs.xml --- a/mothur/tools/mothur/unique.seqs.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/unique.seqs.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Return unique sequences mothur_wrapper.py diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/mothur/venn.xml --- a/mothur/tools/mothur/venn.xml Tue Jun 07 17:32:23 2011 -0400 +++ b/mothur/tools/mothur/venn.xml Tue Jun 07 17:35:35 2011 -0400 @@ -1,4 +1,4 @@ - + Generate Venn diagrams gor groups mothur_wrapper.py @@ -74,6 +74,7 @@ + diff -r 3202a38e44d9 -r fcc0778f6987 mothur/tools/suite_config.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/suite_config.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,237 @@ + + Calculate the number of potentially misaligned bases + + + Align sequences to a template alignment + + + Order Sequences by OTU + + + Generate a newick trees for dissimilarity among groups + + + Find putative chimeras using bellerophon + + + Find putative chimeras using ccode + + + Find putative chimeras using chimeraCheck + + + Find putative chimeras using pintail + + + Find putative chimeras using slayer + + + Trim sequences to a specified length + + + Assign sequences to taxonomy + + + Assign sequences to taxonomy + + + Generate a tree using relaxed neighbor joining + + + Assign sequences to OTUs (Dotur implementation) + + + Group sequences that are part of a larger sequence + + + Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices + + + Assign sequences to OTUs (Operational Taxonomic Unit) + + + Generate collector's curves for calculators on OTUs + + + Summary of calculator values for OTUs + + + Find a consensus sequence for each OTU or phylotype + + + correlation of data to axes + + + Remove gap characters from sequences + + + Return all sequences + + + calculate uncorrected pairwise distances between aligned sequences + + + Generate a phylip-formatted dissimilarity distance matrix among multiple groups + + + Convert fastq to fasta and quality + + + removes columns from alignments + + + Select groups + + + group names from shared or from list and group + + + Picks by taxon + + + Generate a fasta with a representative sequence for each OTU + + + Get otus containing sequences from specified groups + + + Calculate the relative abundance of each otu + + + Picks sequences by name + + + Assign sequences to OTUs (Operational Taxonomic Unit) + + + Generate a heatmap for OTUs + + + Generate a heatmap for pariwise similarity + + + Identify indicator "species" for nodes on a tree + + + Cramer-von Mises tests communities for the same structure + + + Lists the names of the sequences + + + Assign groups to Sets + + + Make a group file + + + Merge data + + + Merge groups in a shared file + + + generate principle components plot data + + + generate non-metric multidimensional scaling data + + + Normalize the number of sequences per group to a specified level + + + calculate uncorrected pairwise distances between sequences + + + Order Sequences by OTU + + + Describes whether two or more communities have the same structure + + + generate principle components plot data + + + Principal Coordinate Analysis + + + Alpha Diversity calculate unique branch length + + + Assign sequences to OTUs based on taxonomy + + + Remove sequences due to pyrosequencing errors + + + Generate inter-sample rarefaction curves for OTUs + + + Generate intra-sample rarefaction curves for OTUs + + + Read OTU list and group to create a shared file + + + Remove groups + + + Picks by taxon + + + Remove otus containing sequences from specified groups + + + Remove rare OTUs + + + Remove sequences by name + + + Reverse complement the sequences + + + Screen sequences + + + Summarize the quality of sequences + + + Separate sequences into rare and abundant groups + + + Generates a fasta file for each group + + + Create a sub sample + + + Summarize the quality of sequences + + + Summary of calculator values for OTUs + + + Summary of calculator values for OTUs + + + Generate a newick tree for dissimilarity among groups + + + Draw a Phylogenic Tree + + + Trim sequences - primers, barcodes, quality + + + Describes whether two or more communities have the same structure + + + Describes whether two or more communities have the same structure + + + Return unique sequences + + + Generate Venn diagrams gor groups +