diff -r 5c77423823cb -r 49058b1f8d3f mothur/datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/datatypes_conf.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 5c77423823cb -r 49058b1f8d3f mothur/lib/galaxy/datatypes/metagenomics.py --- a/mothur/lib/galaxy/datatypes/metagenomics.py Wed May 16 13:12:05 2012 -0500 +++ b/mothur/lib/galaxy/datatypes/metagenomics.py Tue Dec 04 11:05:19 2012 -0600 @@ -6,11 +6,7 @@ import logging, os, os.path, sys, time, tempfile, shutil, string, glob, re import galaxy.model -from galaxy.datatypes import data from galaxy.datatypes.sniff import * -from galaxy.datatypes import metadata -from galaxy.datatypes import tabular -from galaxy.datatypes import sequence from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.data import Text from galaxy.datatypes.tabular import Tabular @@ -21,10 +17,8 @@ pkg_resources.require("simplejson") import simplejson - log = logging.getLogger(__name__) - ## Mothur Classes class Otu( Text ): @@ -833,6 +827,54 @@ close(fh) return False +class CountTable(Tabular): + MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) + file_ext = 'count_table' + + def __init__(self, **kwd): + """ + A table with first column names and following columns integer counts + # Example 1: + Representative_Sequence total + U68630 1 + U68595 1 + U68600 1 + # Example 2 (with group columns): + Representative_Sequence total forest pasture + U68630 1 1 0 + U68595 1 1 0 + U68600 1 1 0 + U68591 1 1 0 + U68647 1 0 1 + """ + Tabular.__init__( self, **kwd ) + self.column_names = ['name','total'] + + def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ): + try: + data_lines = 0; + fh = open( dataset.file_name ) + line = fh.readline() + if line: + line = line.strip() + colnames = line.split() + if len(colnames) > 1: + dataset.metadata.columns = len( colnames ) + if len(colnames) > 2: + dataset.metadata.groups = colnames[2:] + column_types = ['str'] + for i in range(1,len(colnames)): + column_types.append('int') + dataset.metadata.column_types = column_types + dataset.metadata.comment_lines = 1 + while line: + line = fh.readline() + if not line: break + data_lines += 1 + dataset.metadata.data_lines = data_lines + finally: + close(fh) + class RefTaxonomy(Tabular): file_ext = 'ref.taxonomy' """ @@ -1378,7 +1420,7 @@ MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] ) file_ext = 'qiimeotutable' def init_meta( self, dataset, copy_from=None ): - tabular.Tabular.init_meta( self, dataset, copy_from=copy_from ) + Tabular.init_meta( self, dataset, copy_from=copy_from ) def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): self.set_column_names(dataset) def set_column_names(self, dataset): @@ -1400,7 +1442,7 @@ """ file_ext = 'qiimedistmat' def init_meta( self, dataset, copy_from=None ): - tabular.Tabular.init_meta( self, dataset, copy_from=copy_from ) + Tabular.init_meta( self, dataset, copy_from=copy_from ) def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): self.set_column_names(dataset) def set_column_names(self, dataset): diff -r 5c77423823cb -r 49058b1f8d3f mothur/tool-data/datatypes.conf.xml --- a/mothur/tool-data/datatypes.conf.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tool-data/datatypes.conf.xml Tue Dec 04 11:05:19 2012 -0600 @@ -4,6 +4,7 @@ + @@ -12,11 +13,16 @@ + + + @@ -26,7 +32,7 @@ - + @@ -38,10 +44,47 @@ + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 5c77423823cb -r 49058b1f8d3f mothur/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tool_dependencies.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,38 @@ + + + + + + http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip + chmod u+x Mothur.source/uchime_src/mk + cd Mothur.source && make + + Mothur.source/mothur + $INSTALL_DIR/bin + + + Mothur.source/uchime + $INSTALL_DIR/bin + + + $INSTALL_DIR/bin + 2 + + + + +These links provide information for building the Mothur package in most environments . + +http://www.mothur.org/wiki/Download_mothur + +http://www.mothur.org/wiki/Installation + +http://www.mothur.org/wiki/Makefile_options + + + + + + diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/align.check.xml --- a/mothur/tools/mothur/align.check.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/align.check.xml Tue Dec 04 11:05:19 2012 -0600 @@ -33,7 +33,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/align.seqs.xml --- a/mothur/tools/mothur/align.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/align.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -96,7 +96,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/amova.xml --- a/mothur/tools/mothur/amova.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/amova.xml Tue Dec 04 11:05:19 2012 -0600 @@ -26,7 +26,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/anosim.xml --- a/mothur/tools/mothur/anosim.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/anosim.xml Tue Dec 04 11:05:19 2012 -0600 @@ -26,7 +26,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/bin.seqs.xml --- a/mothur/tools/mothur/bin.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/bin.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -34,7 +34,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/chimera.bellerophon.xml --- a/mothur/tools/mothur/chimera.bellerophon.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.bellerophon.xml Tue Dec 04 11:05:19 2012 -0600 @@ -31,7 +31,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/chimera.ccode.xml --- a/mothur/tools/mothur/chimera.ccode.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.ccode.xml Tue Dec 04 11:05:19 2012 -0600 @@ -64,7 +64,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/chimera.check.xml --- a/mothur/tools/mothur/chimera.check.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.check.xml Tue Dec 04 11:05:19 2012 -0600 @@ -64,7 +64,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/chimera.perseus.xml --- a/mothur/tools/mothur/chimera.perseus.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.perseus.xml Tue Dec 04 11:05:19 2012 -0600 @@ -34,7 +34,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/chimera.pintail.xml --- a/mothur/tools/mothur/chimera.pintail.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.pintail.xml Tue Dec 04 11:05:19 2012 -0600 @@ -122,7 +122,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/chimera.slayer.xml --- a/mothur/tools/mothur/chimera.slayer.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.slayer.xml Tue Dec 04 11:05:19 2012 -0600 @@ -98,7 +98,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/chimera.uchime.xml --- a/mothur/tools/mothur/chimera.uchime.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.uchime.xml Tue Dec 04 11:05:19 2012 -0600 @@ -149,7 +149,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/chop.seqs.xml --- a/mothur/tools/mothur/chop.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chop.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -10,6 +10,7 @@ --keep=$keep $countgaps $short + --processors=8 @@ -26,7 +27,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/classify.otu.xml --- a/mothur/tools/mothur/classify.otu.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/classify.otu.xml Tue Dec 04 11:05:19 2012 -0600 @@ -85,7 +85,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/classify.seqs.xml --- a/mothur/tools/mothur/classify.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/classify.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -121,7 +121,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/classify.tree.xml --- a/mothur/tools/mothur/classify.tree.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/classify.tree.xml Tue Dec 04 11:05:19 2012 -0600 @@ -33,7 +33,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/clearcut.xml --- a/mothur/tools/mothur/clearcut.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/clearcut.xml Tue Dec 04 11:05:19 2012 -0600 @@ -64,7 +64,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/cluster.classic.xml --- a/mothur/tools/mothur/cluster.classic.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/cluster.classic.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Dotur implementation) mothur_wrapper.py @@ -9,6 +9,9 @@ #if $name.__str__ != "None" and len($name.__str__) > 0: --name=$name #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if #if len($method.__str__) > 0: --method=$method #end if @@ -24,6 +27,7 @@ + @@ -54,7 +58,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/cluster.fragments.xml --- a/mothur/tools/mothur/cluster.fragments.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/cluster.fragments.xml Tue Dec 04 11:05:19 2012 -0600 @@ -29,7 +29,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/cluster.split.xml --- a/mothur/tools/mothur/cluster.split.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/cluster.split.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices mothur_wrapper.py @@ -32,6 +32,10 @@ --taxlevel=$splitby.taxlevel #end if --splitmethod=$splitby.splitmethod + $splitby.classic + #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count #end if #if len($method.__str__) > 0: --method=$method @@ -82,8 +86,10 @@ + + @@ -115,7 +121,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/cluster.xml --- a/mothur/tools/mothur/cluster.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/cluster.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Operational Taxonomic Unit) mothur_wrapper.py @@ -14,6 +14,9 @@ --name=$matrix.name #end if #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if $sim #if float($cutoff.__str__) > 0.0: --cutoff=$cutoff @@ -41,6 +44,7 @@ + @@ -72,7 +76,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/collect.shared.xml --- a/mothur/tools/mothur/collect.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/collect.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -85,7 +85,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/collect.single.xml --- a/mothur/tools/mothur/collect.single.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/collect.single.xml Tue Dec 04 11:05:19 2012 -0600 @@ -79,7 +79,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/consensus.seqs.xml --- a/mothur/tools/mothur/consensus.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/consensus.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -56,7 +56,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/cooccurrence.xml --- a/mothur/tools/mothur/cooccurrence.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/cooccurrence.xml Tue Dec 04 11:05:19 2012 -0600 @@ -61,7 +61,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/corr.axes.xml --- a/mothur/tools/mothur/corr.axes.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/corr.axes.xml Tue Dec 04 11:05:19 2012 -0600 @@ -65,7 +65,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/count.groups.xml --- a/mothur/tools/mothur/count.groups.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/count.groups.xml Tue Dec 04 11:05:19 2012 -0600 @@ -7,6 +7,8 @@ --outputdir='$logfile.extra_files_path' #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): --shared=$group + #elif isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('count_table').__class__): + --count=$group #else: --group=$group #end if @@ -21,7 +23,7 @@ #end if - + @@ -47,7 +49,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/count.seqs.xml --- a/mothur/tools/mothur/count.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/count.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,5 +1,5 @@ - counts the number of sequences represented by the representative + (aka make.table) counts the number of sequences represented by the representative mothur_wrapper.py --cmd='count.seqs' @@ -14,6 +14,7 @@ --groups='$grouping.groups' #end if #end if + $large @@ -30,13 +31,14 @@ + - + - mothur + mothur @@ -51,11 +53,12 @@ **Command Documenation** -The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file. If a group_ file is given, it will also provide the group count breakdown. +The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file and generates a count_table_. If a group_ file is given, it will also provide the group count breakdown. .. _name: http://www.mothur.org/wiki/Name_file .. _group: http://www.mothur.org/wiki/Group_file .. _count.seqs: http://www.mothur.org/wiki/Count.seqs +.. _count_table: http://www.mothur.org/wiki/Count_File diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/create.database.xml --- a/mothur/tools/mothur/create.database.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/create.database.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ - + creates a database file from a list, repnames, repfasta and contaxonomy file mothur_wrapper.py @@ -7,7 +7,11 @@ --outputdir='$logfile.extra_files_path' ## --datasetid='$logfile.id' --new_file_path='$__new_file_path__' ## --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy','^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$:tax.summary' - --list=$otu + #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): + --shared=$otu + #else + --list=$otu + #end if --repfasta=$repfasta --repname=$repname --contaxonomy=$contaxonomy @@ -19,7 +23,7 @@ #end if - + - mothur + mothur @@ -53,9 +57,10 @@ **Command Documenation** -The create.database_ command reads a list_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file. +The create.database_ command reads a list_ or shared_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file. .. _list: http://www.mothur.org/wiki/List_file +.. _shared: http://www.mothur.org/wiki/Shared_file .. _create.database: http://www.mothur.org/wiki/Create.database diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/degap.seqs.xml --- a/mothur/tools/mothur/degap.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/degap.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -15,7 +15,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/deunique.seqs.xml --- a/mothur/tools/mothur/deunique.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/deunique.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -17,7 +17,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/deunique.tree.xml --- a/mothur/tools/mothur/deunique.tree.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/deunique.tree.xml Tue Dec 04 11:05:19 2012 -0600 @@ -17,7 +17,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/dist.seqs.xml --- a/mothur/tools/mothur/dist.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/dist.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -49,7 +49,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/dist.shared.xml --- a/mothur/tools/mothur/dist.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/dist.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -118,7 +118,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/fastq.info.xml --- a/mothur/tools/mothur/fastq.info.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/fastq.info.xml Tue Dec 04 11:05:19 2012 -0600 @@ -22,7 +22,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/filter.seqs.xml --- a/mothur/tools/mothur/filter.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/filter.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -57,7 +57,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.coremicrobiome.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/get.coremicrobiome.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,82 @@ + + fraction of OTUs for samples or abundances + + mothur_wrapper.py + #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__, "'^\S+\.core\.microbiome$:'" + $core_microbiome.__str__] + --cmd='get.coremicrobiome' + --outputdir='$logfile.extra_files_path' + #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): + --shared=$otu + #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__): + --relabund=$otu + #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=$groups + #end if + #if len($abundance.__str__) > 0 or len($samples.__str__) > 0: + #if len($abundance.__str__) > 0: + --abundance=$abundance + #end if + #if len($samples.__str__) > 0: + --samples=$samples + #end if + #set results = $results + ["'^\S+\.core\.microbiomelist$:'" + $core_microbiomelist.__str__] + #end if + --result=#echo ','.join($results) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (len(abundance.__str__) > 0 or len(samples.__str__) > 0) + + + + 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.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances. + +.. _get.coremicrobiome: http://www.mothur.org/wiki/Get.coremicrobiome + + + + diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.group.xml --- a/mothur/tools/mothur/get.group.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.group.xml Tue Dec 04 11:05:19 2012 -0600 @@ -15,7 +15,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.groups.xml --- a/mothur/tools/mothur/get.groups.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.groups.xml Tue Dec 04 11:05:19 2012 -0600 @@ -94,7 +94,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.lineage.xml --- a/mothur/tools/mothur/get.lineage.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.lineage.xml Tue Dec 04 11:05:19 2012 -0600 @@ -73,7 +73,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.otulabels.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/get.otulabels.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,69 @@ + + Selects OTU labels + + mothur_wrapper.py + #import re, os.path + #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] + ## adds .pick before the last extension to the input file + --cmd='get.otulabels' + --outputdir='$logfile.extra_files_path' + --accnos=$accnos + #if $constaxonomy_in.__str__ != "None" and len($constaxonomy_in.__str__) > 0: + --constaxonomy=$constaxonomy_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy_in.__str__)) + ":'" + $constaxonomy_out.__str__] + #end if + #if $otucorr_in.__str__ != "None" and len($otucorr_in.__str__) > 0: + --otucorr=$otucorr_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($otucorr_in.__str__)) + ":'" + $otucorr_out.__str__] + #end if + #if $corraxes_in.__str__ != "None" and len($corraxes_in.__str__) > 0: + --corraxes=$corraxes_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($corraxes_in.__str__)) + ":'" + $corraxes_out.__str__] + #end if + --result=#echo ','.join($results) + + + + + + + + + + + + constaxonomy_in != None + + + + otucorr_in != None + + + constaxonomy_in != None + + + + 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.otulabels_ command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected. + +.. _classify.otu: http://www.mothur.org/wiki/Classify.otu +.. _corr.axes: http://www.mothur.org/wiki/Corr.axes +.. _otu.association: http://www.mothur.org/wiki/Otu.association +.. _get.otulabels: http://www.mothur.org/wiki/Get.otulabels + + + diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.otulist.xml --- a/mothur/tools/mothur/get.otulist.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.otulist.xml Tue Dec 04 11:05:19 2012 -0600 @@ -38,7 +38,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.oturep.xml --- a/mothur/tools/mothur/get.oturep.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.oturep.xml Tue Dec 04 11:05:19 2012 -0600 @@ -90,7 +90,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.otus.xml --- a/mothur/tools/mothur/get.otus.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.otus.xml Tue Dec 04 11:05:19 2012 -0600 @@ -55,7 +55,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.rabund.xml --- a/mothur/tools/mothur/get.rabund.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.rabund.xml Tue Dec 04 11:05:19 2012 -0600 @@ -30,7 +30,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.relabund.xml --- a/mothur/tools/mothur/get.relabund.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.relabund.xml Tue Dec 04 11:05:19 2012 -0600 @@ -42,7 +42,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.sabund.xml --- a/mothur/tools/mothur/get.sabund.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.sabund.xml Tue Dec 04 11:05:19 2012 -0600 @@ -27,7 +27,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.seqs.xml --- a/mothur/tools/mothur/get.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -77,7 +77,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/get.sharedseqs.xml --- a/mothur/tools/mothur/get.sharedseqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.sharedseqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -78,7 +78,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/hcluster.xml --- a/mothur/tools/mothur/hcluster.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/hcluster.xml Tue Dec 04 11:05:19 2012 -0600 @@ -76,7 +76,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/heatmap.bin.xml --- a/mothur/tools/mothur/heatmap.bin.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/heatmap.bin.xml Tue Dec 04 11:05:19 2012 -0600 @@ -102,7 +102,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/heatmap.sim.xml --- a/mothur/tools/mothur/heatmap.sim.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/heatmap.sim.xml Tue Dec 04 11:05:19 2012 -0600 @@ -86,7 +86,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/homova.xml --- a/mothur/tools/mothur/homova.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/homova.xml Tue Dec 04 11:05:19 2012 -0600 @@ -26,7 +26,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/indicator.xml --- a/mothur/tools/mothur/indicator.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/indicator.xml Tue Dec 04 11:05:19 2012 -0600 @@ -51,7 +51,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/libshuff.xml --- a/mothur/tools/mothur/libshuff.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/libshuff.xml Tue Dec 04 11:05:19 2012 -0600 @@ -52,7 +52,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/list.otulabels.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/list.otulabels.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,66 @@ + + Lists otu labels from shared or relabund file + + mothur_wrapper.py + --cmd='list.otulabels' + --outputdir='$logfile.extra_files_path' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.otulabels$:'$otulabels + #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): + --shared=$otu + #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__): + --relabund=$otu + #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 + + + + + + + + + + + + + + + + + + + + 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 list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otulabels_ or remove.otulabels_ commands. + +.. _list.otulabels: http://www.mothur.org/wiki/List.otulabels +.. _classify.otu: http://www.mothur.org/wiki/Classify.otu +.. _otu.association: http://www.mothur.org/wiki/Otu.association +.. _corr.axes: http://www.mothur.org/wiki/Corr.axes +.. _get.otulabels: http://www.mothur.org/wiki/Get.otulabels +.. _remove.otulabels: http://www.mothur.org/wiki/Remove.otulabels +.. _shared: http://www.mothur.org/wiki/Shared_file +.. _relabund: http://www.mothur.org/wiki/Get.relabund + + + + diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/list.seqs.xml --- a/mothur/tools/mothur/list.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/list.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -55,7 +55,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/make.biom.xml --- a/mothur/tools/mothur/make.biom.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.biom.xml Tue Dec 04 11:05:19 2012 -0600 @@ -45,7 +45,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/make.contigs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/make.contigs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,106 @@ + + Aligns paired forard and reverse fastq files to contigs as fasta and quality + + mothur_wrapper.py + --cmd='make.contigs' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.contigs\.fasta$:'$fasta,'^\S+\.contigs\.qual$:'$qual,'^\S+\.contigs\.mismatch$:'$mismatch + --outputdir='$logfile.extra_files_path' + --ffastq=$ffastq + --rfastq=$rfastq + --align=$align + #if $oligo.add == "yes": + --oligos=$oligo.oligos + #if $oligo.bdiffs.__str__ != '' and int($oligo.bdiffs.__str__) > 0: + --bdiffs=$oligo.bdiffs + #end if + #if $oligo.pdiffs.__str__ != '' and int($oligo.pdiffs.__str__) > 0: + --pdiffs=$oligo.pdiffs + #end if + #if $oligo.tdiffs.__str__ != '' and int($oligo.tdiffs.__str__) > 0: + --tdiffs=$oligo.tdiffs + #end if + #end if + + #if $match.__str__ != '': + --match=$match + #end if + #if $mismatch.__str__ != '': + --mismatch=$mismatch + #end if + #if $gapopen.__str__ != '': + --gapopen=$gapopen + #end if + #if $gapextend.__str__ != '': + --gapextend=$gapextend + #end if + #if $threshold.__str__ != '': + --threshold=$threshold + #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 make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files. + +.. _make.contigs: http://www.mothur.org/wiki/Make.contigs + + + diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/make.design.xml --- a/mothur/tools/mothur/make.design.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.design.xml Tue Dec 04 11:05:19 2012 -0600 @@ -29,7 +29,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/make.fastq.xml --- a/mothur/tools/mothur/make.fastq.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.fastq.xml Tue Dec 04 11:05:19 2012 -0600 @@ -24,7 +24,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/make.group.xml --- a/mothur/tools/mothur/make.group.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.group.xml Tue Dec 04 11:05:19 2012 -0600 @@ -21,7 +21,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/make.shared.xml --- a/mothur/tools/mothur/make.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -48,7 +48,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/make.shared_from_biom.xml --- a/mothur/tools/mothur/make.shared_from_biom.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.shared_from_biom.xml Tue Dec 04 11:05:19 2012 -0600 @@ -31,7 +31,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/mantel.xml --- a/mothur/tools/mothur/mantel.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/mantel.xml Tue Dec 04 11:05:19 2012 -0600 @@ -27,7 +27,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/merge.files.xml --- a/mothur/tools/mothur/merge.files.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/merge.files.xml Tue Dec 04 11:05:19 2012 -0600 @@ -54,7 +54,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/merge.groups.xml --- a/mothur/tools/mothur/merge.groups.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/merge.groups.xml Tue Dec 04 11:05:19 2012 -0600 @@ -85,7 +85,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/metastats.xml --- a/mothur/tools/mothur/metastats.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/metastats.xml Tue Dec 04 11:05:19 2012 -0600 @@ -55,7 +55,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/mothur_wrapper.py --- a/mothur/tools/mothur/mothur_wrapper.py Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/mothur_wrapper.py Tue Dec 04 11:05:19 2012 -0600 @@ -4,7 +4,7 @@ http://www.mothur.org/ Supports mothur version -mothur v.1.24.0 +mothur v.1.27.0 Class encapsulating Mothur galaxy tool. Expect each invocation to include: @@ -195,10 +195,10 @@ cmd_dict['classify.tree'] = dict({'required' : ['taxonomy','tree'],'optional' : ['name','group','cutoff']}) #clear.memory ## not needed in galaxy framework cmd_dict['clearcut'] = dict({'required' : [['phylip','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']}) - cmd_dict['cluster'] = dict({'required' : [['phylip','column']] , 'optional' : ['name','method','cutoff','hard','precision','sim','showabund','timing']}) - cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','method','cutoff','hard','sim','precision']}) + cmd_dict['cluster'] = dict({'required' : [['phylip','column']] , 'optional' : ['name','count','method','cutoff','hard','precision','sim','showabund','timing']}) + cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','count','method','cutoff','hard','sim','precision']}) 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['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','count','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','classic','timing','processors']}) cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']}) 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']}) @@ -206,10 +206,10 @@ cmd_dict['cooccurrence'] = dict({'required' : ['shared'], 'optional' : ['iters','metric','matrixmodel','groups','label']}) 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['count.groups'] = dict({'required' : [['group','shared','count']], 'optional' : ['accnos','groups']}) + cmd_dict['count.seqs'] = dict({'required' : ['name'], 'optional' : ['group','groups','large']}) - cmd_dict['create.database'] = dict({'required' : ['list, repfasta','repname','contaxonomy'], 'optional' : ['group','label']}) + cmd_dict['create.database'] = dict({'required' : [['list','shared'],'repfasta','repname','contaxonomy'], 'optional' : ['group','label']}) cmd_dict['degap.seqs'] = dict({'required' : ['fasta']}) cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []}) @@ -238,6 +238,7 @@ cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]}) cmd_dict['make.biom'] = dict({'required' : ['shared'] , 'optional' : ['contaxonomy','matrixtype','groups','label']}) + cmd_dict['make.contigs'] = dict({'required' : ['ffastq','rfastq',], 'optional' : ['align','match','mismatch','gapopen','gapextend','threshold','oligos','bdiffs','pdiffs','tdiffs','processors']}) cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []}) cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []}) @@ -248,7 +249,7 @@ cmd_dict['metastats'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']}) cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']}) cmd_dict['normalize.shared'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','method','norm','groups','makerelabund']}) - cmd_dict['otu.association'] = dict({'required' : [['shared','relabund']], 'optional' : ['groups', 'label','method']}) + cmd_dict['otu.association'] = dict({'required' : [['shared','relabund']], 'optional' : ['groups', 'label','method','metadata']}) cmd_dict['otu.hierarchy'] = dict({'required' : ['list','label'], 'optional' : ['output']}) cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']}) cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']}) @@ -261,7 +262,7 @@ 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','group','processors']}) - cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble']}) + cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble','design','sets','groupmode']}) 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','design']}) cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) @@ -273,7 +274,7 @@ 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['shhh.flows'] = dict({'required' : [['flow','files']], 'optional' : ['lookup','maxiter','mindelta','cutoff','sigma','order','large','processors']}) cmd_dict['shhh.seqs'] = dict({'required' : [['fasta','files']], 'optional' : ['group','sigma','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']}) @@ -331,6 +332,8 @@ parser.add_option( '--numbases', dest='numbases', type="int", help='Number of base to allow' ) parser.add_option( '--fasta', dest='fasta', help='fasta file paths' ) parser.add_option( '--fastq', dest='fastq', help='fastq file paths' ) + parser.add_option( '--ffastq', dest='ffastq', help='forward fastq file' ) + parser.add_option( '--rfastq', dest='rfastq', help='reverse fastq file' ) parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' ) parser.add_option( '--repfasta', dest='repfasta', help='fasta file paths' ) parser.add_option( '--qaverage', dest='qaverage', type="int", help='Remove sequences that have an average quality below the value' ) @@ -401,6 +404,7 @@ parser.add_option( '--soft', dest='soft', type='int', help='Soft Mask - percentage required to retain column. (0-100)' ) parser.add_option( '--hard', dest='hard', help='Hard Column Filter - A file should only contain one line consisting of 0 and 1 chars' ) parser.add_option( '--calc', dest='calc', help='Calc Method - Gap Penality' ) + parser.add_option( '--count', dest='count', help='Count file' ) parser.add_option( '--countends', dest='countends', help='Penalize terminal gaps' ) parser.add_option( '--cutoff', dest='cutoff', help='Distance Cutoff threshold, discard larger distances' ) parser.add_option( '--countgaps', dest='countgaps', help='count gaps as bases' ) @@ -515,6 +519,7 @@ parser.add_option( '--matrixtype', dest='matrixtype', help='' ) parser.add_option( '--consensus', dest='consensus', help='boolean' ) parser.add_option( '--biom', dest='biom', help='biom file' ) + parser.add_option( '--classic', dest='classic', help='boolean' ) # include read.otu options parser.add_option( '--rabund', dest='rabund', help='' ) parser.add_option( '--sabund', dest='sabund', help='' ) @@ -653,10 +658,21 @@ if re.match(pattern,line): chimera_count += 1 info += "Chimeras: %d" % chimera_count + elif options.cmd == 'count.groups': + fh = open(os.path.join(outputdir,'tmp.groups.count'),'w') + for line in tmp_stdout: + m = re.match('(.+) contains (\d+)\.',line) + if m and len(m.groups()) == 2: + info += line + print >> fh, "%s\t%s\n" % (m.group(1),m.group(2)) + fh.close() else: found_begin = False info_chars = 0 for line in tmp_stdout: + if re.match('mothur > ' + options.cmd + '$.*$', line): + found_begin = True + continue if line.find(outputdir) >= 0: continue if line.startswith('**************'): @@ -671,18 +687,19 @@ continue if re.match('.*\.\.\.\s*$',line): continue - if re.match('^\d*\s*$',line): + if re.match('^\d*\s*$',line) and not line.find(' contains '): continue # if re.match('^(unique|[0-9.]*)(\t\d+)+',line): # abundance from cluster commands - if not options.cmd.startswith('unifrac') and re.match('^(unique|[0-9.]+)(\t\d+)*',line): # abundance from cluster commands, allow unique line into info + if (not (options.cmd.startswith('unifrac') or options.cmd.startswith('count.groups')) + and re.match('^(unique|[0-9.]+)(\t\d+)*',line)): # abundance from cluster commands, allow unique line into info continue if re.match('Output .*',line): break + if re.match('mothur > quit()',line): + break if found_begin and info_chars < 200: info += "%s" % line info_chars += len(line) - if re.match('mothur > ' + options.cmd + '$.*$', line): - found_begin = True tmp_stdout.close() print >> sys.stdout, info # Collect output files diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/nmds.xml --- a/mothur/tools/mothur/nmds.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/nmds.xml Tue Dec 04 11:05:19 2012 -0600 @@ -41,7 +41,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/normalize.shared.xml --- a/mothur/tools/mothur/normalize.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/normalize.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -50,7 +50,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/otu.association.xml --- a/mothur/tools/mothur/otu.association.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/otu.association.xml Tue Dec 04 11:05:19 2012 -0600 @@ -21,6 +21,9 @@ #if $method.__str__ != "None" and len($method.__str__) > 0: --method=$method #end if + #if $metadata.__str__ != "None" and len($method.__str__) > 0: + --metadata=$metadata + #end if @@ -39,12 +42,13 @@ + - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/otu.hierarchy.xml --- a/mothur/tools/mothur/otu.hierarchy.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/otu.hierarchy.xml Tue Dec 04 11:05:19 2012 -0600 @@ -33,7 +33,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/pairwise.seqs.xml --- a/mothur/tools/mothur/pairwise.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/pairwise.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -74,7 +74,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/parse.list.xml --- a/mothur/tools/mothur/parse.list.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/parse.list.xml Tue Dec 04 11:05:19 2012 -0600 @@ -27,7 +27,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/parsimony.xml --- a/mothur/tools/mothur/parsimony.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/parsimony.xml Tue Dec 04 11:05:19 2012 -0600 @@ -47,7 +47,7 @@ --> - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/pca.xml --- a/mothur/tools/mothur/pca.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/pca.xml Tue Dec 04 11:05:19 2012 -0600 @@ -40,7 +40,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/pcoa.xml --- a/mothur/tools/mothur/pcoa.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/pcoa.xml Tue Dec 04 11:05:19 2012 -0600 @@ -18,7 +18,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/pcr.seqs.xml --- a/mothur/tools/mothur/pcr.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/pcr.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -99,7 +99,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/phylo.diversity.xml --- a/mothur/tools/mothur/phylo.diversity.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/phylo.diversity.xml Tue Dec 04 11:05:19 2012 -0600 @@ -74,7 +74,7 @@ --> - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/phylotype.xml --- a/mothur/tools/mothur/phylotype.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/phylotype.xml Tue Dec 04 11:05:19 2012 -0600 @@ -41,7 +41,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/pre.cluster.xml --- a/mothur/tools/mothur/pre.cluster.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/pre.cluster.xml Tue Dec 04 11:05:19 2012 -0600 @@ -36,7 +36,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/rarefaction.shared.xml --- a/mothur/tools/mothur/rarefaction.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/rarefaction.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ - + Generate inter-sample rarefaction curves for OTUs mothur_wrapper.py @@ -12,6 +12,12 @@ #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if + #if $design.use: + --design=$design.design + #if $design.sets.__str__ != '': + --sets='$design.sets' + #end if + #end if #if int($iters.__str__) > 0: --iters=$iters #end if @@ -19,6 +25,18 @@ #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc='$calc' #end if + #if $subsample.use.__str__ == 'yes': + #if $subsample.subsample.__str__ != '': + --subsample=$subsample.subsample + #else + --subsample=T + #end if + #if $subsample.subsampleiters.__str__ != '': + --subsampleiters=$subsample.subsampleiters + #end if + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.ave-std\.((unique|[0-9.]*)(\..*?)+\.shared\.rarefaction)$:tabular' + #end if @@ -31,22 +49,48 @@ All groups will be analyzed by default if none are selected + + + + + + + + + + + + + + + + + + + + + + + - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/rarefaction.single.xml --- a/mothur/tools/mothur/rarefaction.single.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/rarefaction.single.xml Tue Dec 04 11:05:19 2012 -0600 @@ -69,7 +69,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/remove.groups.xml --- a/mothur/tools/mothur/remove.groups.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/remove.groups.xml Tue Dec 04 11:05:19 2012 -0600 @@ -94,7 +94,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/remove.lineage.xml --- a/mothur/tools/mothur/remove.lineage.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/remove.lineage.xml Tue Dec 04 11:05:19 2012 -0600 @@ -73,7 +73,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/remove.otulabels.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/remove.otulabels.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,69 @@ + + Removes OTU labels + + mothur_wrapper.py + #import re, os.path + #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] + ## adds .pick before the last extension to the input file + --cmd='remove.otulabels' + --outputdir='$logfile.extra_files_path' + --accnos=$accnos + #if $constaxonomy_in.__str__ != "None" and len($constaxonomy_in.__str__) > 0: + --constaxonomy=$constaxonomy_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy_in.__str__)) + ":'" + $constaxonomy_out.__str__] + #end if + #if $otucorr_in.__str__ != "None" and len($otucorr_in.__str__) > 0: + --otucorr=$otucorr_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($otucorr_in.__str__)) + ":'" + $otucorr_out.__str__] + #end if + #if $corraxes_in.__str__ != "None" and len($corraxes_in.__str__) > 0: + --corraxes=$corraxes_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($corraxes_in.__str__)) + ":'" + $corraxes_out.__str__] + #end if + --result=#echo ','.join($results) + + + + + + + + + + + + constaxonomy_in != None + + + + otucorr_in != None + + + constaxonomy_in != None + + + + 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.otulabels_ command removes otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected. + +.. _classify.otu: http://www.mothur.org/wiki/Classify.otu +.. _corr.axes: http://www.mothur.org/wiki/Corr.axes +.. _otu.association: http://www.mothur.org/wiki/Otu.association +.. _remove.otulabels: http://www.mothur.org/wiki/Remove.otulabels + + + diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/remove.otus.xml --- a/mothur/tools/mothur/remove.otus.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/remove.otus.xml Tue Dec 04 11:05:19 2012 -0600 @@ -55,7 +55,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/remove.rare.xml --- a/mothur/tools/mothur/remove.rare.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/remove.rare.xml Tue Dec 04 11:05:19 2012 -0600 @@ -91,7 +91,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/remove.seqs.xml --- a/mothur/tools/mothur/remove.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/remove.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -77,7 +77,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/reverse.seqs.xml --- a/mothur/tools/mothur/reverse.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/reverse.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -15,7 +15,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/screen.seqs.xml --- a/mothur/tools/mothur/screen.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/screen.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -101,7 +101,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/sens.spec.xml --- a/mothur/tools/mothur/sens.spec.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/sens.spec.xml Tue Dec 04 11:05:19 2012 -0600 @@ -42,7 +42,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/seq.error.xml --- a/mothur/tools/mothur/seq.error.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/seq.error.xml Tue Dec 04 11:05:19 2012 -0600 @@ -146,7 +146,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/sffinfo.xml --- a/mothur/tools/mothur/sffinfo.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/sffinfo.xml Tue Dec 04 11:05:19 2012 -0600 @@ -53,7 +53,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/shhh.flows.xml --- a/mothur/tools/mothur/shhh.flows.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/shhh.flows.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ - + Denoise flowgrams (PyroNoise algorithm) mothur_wrapper.py @@ -23,6 +23,9 @@ #if $order.__str__.strip() != '': --order=$order #end if + #if $large.__str__ != '': + --large=$large + #end if --processors=8 @@ -69,6 +72,10 @@ + + + + @@ -79,7 +86,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/shhh.seqs.xml --- a/mothur/tools/mothur/shhh.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/shhh.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -32,7 +32,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/sort.seqs.xml --- a/mothur/tools/mothur/sort.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/sort.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -69,7 +69,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/split.abund.xml --- a/mothur/tools/mothur/split.abund.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/split.abund.xml Tue Dec 04 11:05:19 2012 -0600 @@ -98,7 +98,7 @@ --> - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/split.groups.xml --- a/mothur/tools/mothur/split.groups.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/split.groups.xml Tue Dec 04 11:05:19 2012 -0600 @@ -30,7 +30,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/sub.sample.xml --- a/mothur/tools/mothur/sub.sample.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/sub.sample.xml Tue Dec 04 11:05:19 2012 -0600 @@ -179,7 +179,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/summary.qual.xml --- a/mothur/tools/mothur/summary.qual.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/summary.qual.xml Tue Dec 04 11:05:19 2012 -0600 @@ -20,7 +20,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/summary.seqs.xml --- a/mothur/tools/mothur/summary.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/summary.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -20,7 +20,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/summary.shared.xml --- a/mothur/tools/mothur/summary.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/summary.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ - + Summary of calculator values for OTUs mothur_wrapper.py @@ -6,7 +6,6 @@ --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist' --shared=$otu #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups @@ -19,6 +18,29 @@ #end if $all $distance + #if $subsample.use.__str__ == 'yes': + #if $subsample.subsample.__str__ != '': + --subsample=$subsample.subsample + #else + --subsample=T + #end if + #if $subsample.iters.__str__ != '': + --iters=$subsample.iters + #end if + #if len($subsample.output.__str__) > 0: + --output=$subsample.output + #end if + #if $subsample.as_datasets.__str__ == 'yes': + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + #if $subsample.output.__str__ == 'square': + ## patient70.fn.jest.0.16.lt.ave.dist + --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)(\.(ave|std))?\.dist)$:square.dist' + #else + ## patient70.fn.jest.0.13.square.std.dist + --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)(\.(ave|std))?\.dist)$:lower.dist' + #end if + #end if + #end if --processors=8 @@ -77,13 +99,29 @@ + + + + + + + + + + + + + + - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/summary.single.xml --- a/mothur/tools/mothur/summary.single.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/summary.single.xml Tue Dec 04 11:05:19 2012 -0600 @@ -8,7 +8,11 @@ --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+\.((\S+?)\.summary)$:tabular' #else: - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary + #if $subsample.use.__str__ == 'yes': + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.groups\.ave-std\.summary$:'$subsample_summary,'^\S+\.groups\.summary$:'$summary, + #else + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary + #end if #end if --outputdir='$logfile.extra_files_path' #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): @@ -33,6 +37,16 @@ #if int($size.__str__) > 0: --size=$size #end if + #if $subsample.use.__str__ == 'yes': + #if $subsample.subsample.__str__ != '': + --subsample=$subsample.subsample + #else + --subsample=T + #end if + #if $subsample.iters.__str__ != '': + --iters=$subsample.iters + #end if + #end if @@ -70,6 +84,15 @@ + + + + + + + + @@ -79,9 +102,12 @@ (otu.file_ext == 'shared' and groupmode == True) + + (subsample['use'] and not (otu.file_ext == 'shared' and groupmode == False)) + - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/summary.tax.xml --- a/mothur/tools/mothur/summary.tax.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/summary.tax.xml Tue Dec 04 11:05:19 2012 -0600 @@ -61,7 +61,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/tree.shared.xml --- a/mothur/tools/mothur/tree.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/tree.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -136,7 +136,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/trim.flows.xml --- a/mothur/tools/mothur/trim.flows.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/trim.flows.xml Tue Dec 04 11:05:19 2012 -0600 @@ -115,7 +115,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/trim.seqs.xml --- a/mothur/tools/mothur/trim.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/trim.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -151,7 +151,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/unifrac.unweighted.xml --- a/mothur/tools/mothur/unifrac.unweighted.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/unifrac.unweighted.xml Tue Dec 04 11:05:19 2012 -0600 @@ -110,7 +110,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/unifrac.weighted.xml --- a/mothur/tools/mothur/unifrac.weighted.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/unifrac.weighted.xml Tue Dec 04 11:05:19 2012 -0600 @@ -117,7 +117,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/unique.seqs.xml --- a/mothur/tools/mothur/unique.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/unique.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -20,7 +20,7 @@ - mothur + mothur diff -r 5c77423823cb -r 49058b1f8d3f mothur/tools/mothur/venn.xml --- a/mothur/tools/mothur/venn.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/venn.xml Tue Dec 04 11:05:19 2012 -0600 @@ -88,7 +88,7 @@ - mothur + mothur