# HG changeset patch # User certain cat # Date 1414782572 14400 # Node ID 95d75b35e4d21474195a9489ff527576ee2cee1e # Parent 1be61ceb20d7790b99225245c1b67a85bfe0064e Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes) diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/README --- a/mothur/README Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/README Fri Oct 31 15:09:32 2014 -0400 @@ -1,15 +1,27 @@ Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page + Mothur should be able to be auto-installed as a tool_dependency You may want to reorganize the tool panel after installing See below: Reorganize integrated_tool_panel.xml This was based on: http://www.mothur.org/wiki/Mothur_manual (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used for mothur commands) This will be set in: tool_dependencies/mothur/1.27/jjohnson/mothur_toolsuite/*/env.sh + Requirements for auto installation: + - make (sudo-apt get install make) + - g++ (sudo apt-get install g++) + - gfortran (sudo apt-get install gfortran) + - pip (sudo apt-get install python-pip) + - simplejson (pip install simplejson) + + Repository Dependency: + - BLAST Legacy ver. 2.2.26 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/) + - The repository name should be package_blast_2_2_26 so it matches with the tool dependency. + Manual installation for Mothur: - Install mothur v.1.27 on your galaxy system so galaxy can execute the mothur command - ( This version of wrappers is designed for Mothur version 1.27 - it may work on later versions ) + Install mothur v.1.33 on your galaxy system so galaxy can execute the mothur command + ( This version of wrappers is designed for Mothur version 1.33- it may work on later versions ) http://www.mothur.org/wiki/Download_mothur http://www.mothur.org/wiki/Installation ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode ) @@ -126,292 +138,8 @@ add datatypes to: datatypes_conf.xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Reorganize integrated_tool_panel.xml : -
-
- - add mothur tools to: tool_conf.xml -
-
############ DESIGN NOTES ######################################################################################################### Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/datatypes_conf.xml --- a/mothur/datatypes_conf.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/datatypes_conf.xml Fri Oct 31 15:09:32 2014 -0400 @@ -50,6 +50,8 @@ + + @@ -75,6 +77,8 @@ + + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/lib/galaxy/datatypes/metagenomics.py --- a/mothur/lib/galaxy/datatypes/metagenomics.py Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/lib/galaxy/datatypes/metagenomics.py Fri Oct 31 15:09:32 2014 -0400 @@ -22,6 +22,7 @@ ## Mothur Classes class Otu( Text ): + file_ext = 'otu' MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0 ) MetadataElement( name="labels", default=[], desc="Label Names", readonly=True, visible=True, no_value=[] ) @@ -752,6 +753,127 @@ finally: fh.close() return False +""" +class OtuMap( Tabular ): + file_ext = 'otu_map' + + def __init__(self, **kwd): + Tabular.__init__(self,**kwd) + self.column_names = ['catdog','dog'] + self.column_types = ['int','float'] + + def sniff(self, filename): #sniffer that detects whether it's an otu table. + #it appears that self refers to the object passed in, and filename will be the name of the file? + try: + fh = open( filename) + line = fh.readline() + line = line.strip() + if line[0] != '#': + return False + count=0 + while True: + #go thru the file. + line = fh.readline() + line = line.strip() + if not line: + break + else: + if line[0] != '#': + try: + linePieces = line.split('\t') + i = int(linePieces[0]) + f = float(linePieces[1]) + continue + except: + return False + #went through the file, can split! + return True + except: + #failed to open file ? + pass + finally: + fh.close() + #at this point we might as well return false.. + return False +""" +class Metadata ( Tabular ): + file_ext='metadata' + """ + group dpw description + F003D000 0 "F003D000 description" + F003D002 2 "F003D002 description" + F003D004 4 "F003D004 description" + F003D006 6 "F003D006 description" + F003D008 8 "F003D008 description" + F003D142 142 "F003D142 description" + F003D144 144 "F003D144 description" + F003D146 146 "F003D146 description" + F003D148 148 "F003D148 description" + F003D150 150 "F003D150 description" + MOCK.GQY1XT001 12 "MOCK.GQY1XT001 description" + """ + def __init__(self, **kwd): + Tabular.__init__( self, **kwd ) + self.column_names = ['group','dpw','description'] + self.column_types = ['string','int','string'] + + def sniff (self,filename): + try: + fh = open (filename) + line = fh.readline() + line = line.strip() + headers = line.split('\t') + #check the header for the needed + if headers[0] == "group" and headers[1] == "dpw" and headers[2] == "description": + return True + except: + pass + finally: + fh.close() + return False + + + +class OtuMap(Tabular): + file_ext = 'otu_map' + def __init__(self, **kwd): + """A list of names""" + Tabular.__init__( self, **kwd ) + self.column_names = ['OTU','SEQIDS'] + self.column_types = ['int','float'] + + def sniff( self, filename ): + """ + Determines whether the file is a frequency tabular format for chimera analysis + #1.14.0 + 0 0.000 + 1 0.000 + ... + 155 0.975 + """ + try: + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + else: + if line[0] != '#': + try: + linePieces = line.split('\t') + i = int(linePieces[0]) + continue + except: + return False + return True + except: + pass + finally: + fh.close() + return False + class Frequency(Tabular): file_ext = 'freq' @@ -772,6 +894,11 @@ """ try: fh = open( filename ) + #checks first line for # + line = fh.readline() + line = line.strip() + if line[0] != '#': + return False count = 0 while True: line = fh.readline() @@ -1400,7 +1527,6 @@ fh.close() return False - ## Biom class BiologicalObservationMatrix( Text ): diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tool-data/datatypes.conf.xml --- a/mothur/tool-data/datatypes.conf.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tool-data/datatypes.conf.xml Fri Oct 31 15:09:32 2014 -0400 @@ -39,6 +39,7 @@ + @@ -75,6 +76,7 @@ + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tool_dependencies.xml --- a/mothur/tool_dependencies.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tool_dependencies.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,44 +1,122 @@ - + - - - - http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip - - sed -i 's/^USECOMPRESSION ?= no/USECOMPRESSION ?= yes/' Mothur.source/makefile - sed -i 's/TARGET_ARCH += -arch x86_64/#TARGET_ARCH += -arch x86_64/' Mothur.source/makefile - sed -i 's/#CXXFLAGS +=/CXXFLAGS +=/' Mothur.source/makefile - - sed -i 's/LINK_OPTS=-static/LINK_OPTS=/' Mothur.source/uchime_src/mk - 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/w/images/6/65/Mothur.1.33.3.zip + chmod u+x Mothur.source/uchime_src/mk + + + test $(uname) = Linux && + perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' Mothur.source/makefile || + true + + cd Mothur.source; make -j 2; + + Mothur.source/mothur + $INSTALL_DIR/bin + + + Mothur.source/uchime + $INSTALL_DIR/bin + + + $INSTALL_DIR/bin + 2 + + + + + + - - - - + + $INSTALL_DIR/bin/blast + $INSTALL_DIR/bin/blast/bin + $INSTALL_DIR/bin + + + cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin + + + + + + Iyad Kandalaft added shell commands to build in Linux environment such as Redhat/Centos/Ubuntu. ReadLine libraries are not required. libncurses-devel are required. + + These links provide information for building the Mothur package in most environments . + + http://www.mothur.org/wiki/Download_mothur + http://www.mothur.org/wiki/Installation + + http://www.mothur.org/wiki/Makefile_options + + + + + + + + + + + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/align.check.xml --- a/mothur/tools/mothur/align.check.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/align.check.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Calculate the number of potentially misaligned bases mothur_wrapper.py @@ -6,7 +6,14 @@ --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align\.check$:'$out_file --outputdir='$logfile.extra_files_path' --fasta=$fasta - --map=$ss.map + --map=$ss.map + #if $count.__str__ != "None" and len($count.__str__) >0: + --count=$count + #end if + #if $count.__str__ != "None" and len($count.__str__) >0: + --name=$name + #end if + @@ -17,23 +24,23 @@ - - - + - + + + - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/align.seqs.xml --- a/mothur/tools/mothur/align.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/align.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Align sequences to a template alignment mothur_wrapper.py @@ -34,9 +34,7 @@ - - - + @@ -96,7 +94,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/amova.xml --- a/mothur/tools/mothur/amova.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/amova.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Analysis of molecular variance mothur_wrapper.py @@ -12,21 +12,29 @@ #end if #if float($alpha.__str__) > 0.0: --alpha=$alpha - #end if + #end if + #if $sets.__str__ != "None" and len ($sets.__str__) >0: + --sets=$sets + #end if - + + + + + + - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/anosim.xml --- a/mothur/tools/mothur/anosim.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/anosim.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Non-parametric multivariate analysis of changes in community structure mothur_wrapper.py @@ -26,7 +26,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/bin.seqs.xml --- a/mothur/tools/mothur/bin.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/bin.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,58 +1,63 @@ - - Order Sequences by OTU - - mothur_wrapper.py - --cmd='bin.seqs' - --result='^mothur.\S+\.logfile$:'$logfile - --outputdir='$logfile.extra_files_path' - --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:${fasta.ext}' - --fasta=$fasta - --list=$otu - #if $name.__str__ != "None" and len($name.__str__) > 0: - --name=$name - #end if - #if $label.__str__ != "None" and len($label.__str__) > 0: - --label='$label' - #end if - #if $group.__str__ != "None" and len($group.__str__) > 0: - --group='$group' - #end if - - - - - - - - - - - - - - - - - mothur - - - - -**Mothur Overview** + + Order Sequences by OTU + + mothur_wrapper.py + --cmd='bin.seqs' + --result='^mothur.\S+\.logfile$:'$logfile + --outputdir='$logfile.extra_files_path' + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:${fasta.ext}' + --fasta=$fasta + --list=$otu + #if $name.__str__ != "None" and len($name.__str__) > 0: + --name=$name + #end if + #if $label.__str__ != "None" and len($label.__str__) > 0: + --label='$label' + #end if + #if $group.__str__ != "None" and len($group.__str__) > 0: + --group='$group' + #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count='$count' + #end if -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** + + + + + + + + + + + + + + + + + + mothur + + + + + **Mothur Overview** -The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences. + 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** -.. _list_file: http://www.mothur.org/wiki/List_file -.. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs + The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences. - + .. _list_file: http://www.mothur.org/wiki/List_file + .. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs + + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/chimera.bellerophon.xml --- a/mothur/tools/mothur/chimera.bellerophon.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.bellerophon.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using bellerophon mothur_wrapper.py @@ -31,7 +31,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/chimera.ccode.xml --- a/mothur/tools/mothur/chimera.ccode.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.ccode.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using ccode mothur_wrapper.py @@ -30,9 +30,7 @@ - - - + @@ -64,7 +62,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/chimera.check.xml --- a/mothur/tools/mothur/chimera.check.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.check.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using chimeraCheck mothur_wrapper.py @@ -34,9 +34,7 @@ - - - + @@ -64,7 +62,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/chimera.perseus.xml --- a/mothur/tools/mothur/chimera.perseus.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.perseus.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using chimeraCheck mothur_wrapper.py @@ -7,7 +7,11 @@ --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file,'^\S+\.perseus\.accnos$:'$out_accnos --outputdir='$logfile.extra_files_path' --fasta=$fasta - --name=$name + #if isinstance($name.datatype, $__app__.datatypes_registry.get_datatype_by_extension('name').__class__): + --name=$name + #else + --count=$name + #end if #if $group.__str__ != "None" and len($group.__str__) > 0: --group='$group' #end if @@ -21,14 +25,16 @@ --cutoff=$cutoff #end if --processors=8 + $dereplicate - + + @@ -36,7 +42,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/chimera.pintail.xml --- a/mothur/tools/mothur/chimera.pintail.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.pintail.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using pintail mothur_wrapper.py @@ -44,9 +44,7 @@ - - - + @@ -122,7 +120,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/chimera.slayer.xml --- a/mothur/tools/mothur/chimera.slayer.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.slayer.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using slayer mothur_wrapper.py @@ -14,7 +14,10 @@ #end if #if $alignment.group.__str__ != '': --group=$alignment.group - #end if + #end if + #if $alignment.count.__str__ != '': + --count=$alignment.count + #end if #else: --reference=$alignment.template #end if @@ -36,7 +39,8 @@ $options.split #end if ## --blastlocation=path_to_blast - --processors=8 + --processors=8 + $dereplicate @@ -48,16 +52,15 @@ - - - + - - + + + @@ -90,7 +93,11 @@ - + + + + + @@ -98,7 +105,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/chimera.uchime.xml --- a/mothur/tools/mothur/chimera.uchime.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.uchime.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Find putative chimeras using uchime mothur_wrapper.py @@ -26,6 +26,9 @@ #if $template.group.__str__ != '': --group=$template.group #end if + #if $template.count.__str__ != '': + --count=$template.count + #end if #elif $template.source == 'names': --name=$template.name #end if @@ -69,10 +72,11 @@ $skipgaps2 #if $alignment.ucl: --ucl=true - #if $alignment.queryfract != None and len($alignment.queryfract) > 0 and 1.0 >= float($alignment.queryfract) > 0: + #if $alignment.queryfract != "None" and len($alignment.queryfract) > 0 and 1.0 >= float($alignment.queryfract) > 0: --queryfract=$alignment.queryfract #end if #end if + $dereplicate $chimealns --processors=8 @@ -87,9 +91,7 @@ - - - + @@ -100,6 +102,8 @@ + @@ -107,6 +111,8 @@ + + @@ -149,7 +155,7 @@ - mothur + mothur @@ -168,6 +174,7 @@ .. _chimera.uchime: http://www.mothur.org/wiki/Chimera.uchime +Version 1.23.0: Upgrades tool dependency to mothur 1.33 and adds support for count (mothur 1.28) and dereplicate (mothur 1.29) options. diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/chop.seqs.xml --- a/mothur/tools/mothur/chop.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chop.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Trim sequences to a specified length mothur_wrapper.py @@ -10,7 +10,16 @@ --keep=$keep $countgaps $short - --processors=8 + --processors=8 + #if $name.__str__ != "None": + --name=$name + #end if + #if $group.__str__ != "None": + --group=$group + #end if + #if $count.__str__ != "None": + --count=$count + #end if @@ -21,13 +30,16 @@ + + + - mothur + mothur @@ -46,6 +58,7 @@ .. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs +v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0 diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/classify.otu.xml --- a/mothur/tools/mothur/classify.otu.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/classify.otu.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to taxonomy mothur_wrapper.py @@ -12,7 +12,10 @@ #if $name.__str__ != "None" and len($name.__str__) > 0: --name='$name' #end if - #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0: + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count='$count' + #end if + #if $reftax.source != 'None' and len($reftax.taxonomy.__str__) > 0: --reftaxonomy=$reftax.taxonomy #end if #if 100 >= int($cutoff.__str__) > 0: @@ -25,11 +28,13 @@ --group='$group' #end if --basis=$basis - $probs + $probs + $persample + @@ -37,9 +42,7 @@ - - - + @@ -49,16 +52,14 @@ - + - + - - - + @@ -80,12 +81,13 @@ + - mothur + mothur @@ -106,6 +108,6 @@ .. _classify.otu: http://www.mothur.org/wiki/Classify.otu - +v1.21.0: Updated to use Mothur 1.33. Added count parameter (1.28.0) and persample parameter (1.29.0) diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/classify.seqs.xml --- a/mothur/tools/mothur/classify.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/classify.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,119 +1,125 @@ - - Assign sequences to taxonomy - - mothur_wrapper.py - --cmd='classify.seqs' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.taxonomy$:'$taxonomy_out,'^\S+\.tax\.summary$:'$tax_summary - --outputdir='$logfile.extra_files_path' - --fasta=$fasta - --reference=$alignment.template - --taxonomy=$tax.taxonomy - #if $classify.method == 'bayesian': - --method=$classify.method - #if 15 >= int($classify.ksize.__str__) >= 4: - --ksize=$classify.ksize - #end if - #if int($classify.iters.__str__) > 0: - --iters=$classify.iters - #end if - #if 100 >= int($classify.cutoff.__str__) > 0: - --cutoff=$classify.cutoff - #end if - $classify.probs - #elif $classify.method == 'knn': - --method=$classify.method - --numwanted=$classify.search.numwanted - #if $classify.search.algorithm == 'kmer': - --search=$classify.search.algorithm - --ksize=$classify.search.ksize - #elif $classify.search.algorithm == 'blast': - --search=$classify.search.algorithm - --match=$classify.search.match - --mismatch=$classify.search.mismatch - --gapopen=$classify.search.gapopen - --gapextend=$classify.search.gapextend - #elif $classify.knn.search == 'suffix': - --search=$classify.search.algorithm - #elif $classify.search.algorithm == 'distance': - --search=$classify.search.algorithm - #end if - #end if - --processors=8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Assign sequences to taxonomy + + mothur_wrapper.py + --cmd='classify.seqs' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.taxonomy$:'$taxonomy_out,'^\S+\.tax\.summary$:'$tax_summary + --outputdir='$logfile.extra_files_path' + --fasta=$fasta + --reference=$alignment.template + --taxonomy=$tax.taxonomy + #if $classify.method == 'wang': + --method=$classify.method + #if 15 >= int($classify.ksize.__str__) >= 4: + --ksize=$classify.ksize + #end if + #if int($classify.iters.__str__) > 0: + --iters=$classify.iters + #end if + #if 100 >= int($classify.cutoff.__str__) > 0: + --cutoff=$classify.cutoff + #end if + $classify.probs + #elif $classify.method == 'knn': + --method=$classify.method + --numwanted=$classify.search.numwanted + #if $classify.search.algorithm == 'kmer': + --search=$classify.search.algorithm + --ksize=$classify.search.ksize + #elif $classify.search.algorithm == 'blast': + --search=$classify.search.algorithm + --match=$classify.search.match + --mismatch=$classify.search.mismatch + --gapopen=$classify.search.gapopen + --gapextend=$classify.search.gapextend + #elif $classify.knn.search == 'suffix': + --search=$classify.search.algorithm + #elif $classify.search.algorithm == 'distance': + --search=$classify.search.algorithm + #end if + #end if + --processors=8 + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + $relabund + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -121,7 +127,7 @@ - mothur + mothur @@ -141,5 +147,7 @@ .. _classify.seqs: http://www.mothur.org/wiki/Classify.seqs +v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang. + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/classify.tree.xml --- a/mothur/tools/mothur/classify.tree.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/classify.tree.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Get a consensus taxonomy for each node on a tree mothur_wrapper.py @@ -33,7 +33,7 @@ - mothur + mothur @@ -65,6 +65,7 @@ .. _group: http://www.mothur.org/wiki/Group_file .. _classify.tree: http://www.mothur.org/wiki/Classify.tree +v.1.25.0: Trivial upgrade to Mothur 1.33 diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/clearcut.xml --- a/mothur/tools/mothur/clearcut.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/clearcut.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Generate a tree using relaxed neighbor joining mothur_wrapper.py @@ -64,7 +64,7 @@ - mothur + mothur @@ -90,5 +90,7 @@ .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/ .. _clearcut: http://www.mothur.org/wiki/Clearcut +v.1.20.0: Trivial upgrade to Mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/cluster.classic.xml --- a/mothur/tools/mothur/cluster.classic.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/cluster.classic.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Dotur implementation) mothur_wrapper.py @@ -58,7 +58,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/cluster.fragments.xml --- a/mothur/tools/mothur/cluster.fragments.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/cluster.fragments.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,53 +1,60 @@ - - Group sequences that are part of a larger sequence - - mothur_wrapper.py - --cmd='cluster.fragments' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fragclust\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names - --outputdir='$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 - - - - - - - - - - - - - - - - mothur - - - - -**Mothur Overview** + + Group sequences that are part of a larger sequence + + mothur_wrapper.py + --cmd='cluster.fragments' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fragclust\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names + --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 +#if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count +#end if + + + + + + + + + + + + + + + + + mothur + + + + + **Mothur Overview** -Mothur_, initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. + Mothur_, initiated by Dr. Patrick Schloss and his software development team + in the Department of Microbiology and Immunology at The University of Michigan, + provides bioinformatics for the microbial ecology community. -.. _Mothur: http://www.mothur.org/wiki/Main_Page + .. _Mothur: http://www.mothur.org/wiki/Main_Page -**Command Documenation** + **Command Documenation** + + The cluster.fragments_ command groups sequences that are part of a larger sequence. -The cluster.fragments_ command groups sequences that are part of a larger sequence. + .. _cluster.fragments: http://www.mothur.org/wiki/Cluster.fragments -.. _cluster.fragments: http://www.mothur.org/wiki/Cluster.fragments + v1.21: Updated to Mothur 1.33. Added count parameter. - + + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/cluster.split.xml --- a/mothur/tools/mothur/cluster.split.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/cluster.split.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices mothur_wrapper.py @@ -48,7 +48,8 @@ --precision=$precision #end if $large - --processors=8 + --processors=8 + $cluster @@ -87,7 +88,9 @@ + /> + + @@ -108,8 +111,11 @@ - + + + @@ -121,7 +127,7 @@ - mothur + mothur @@ -140,6 +146,8 @@ .. _cluster.split: http://www.mothur.org/wiki/Cluster.split +v1.28.0: Upgraded to Mothur 1.33, introduced cluster boolean. + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/cluster.xml --- a/mothur/tools/mothur/cluster.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/cluster.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Operational Taxonomic Unit) mothur_wrapper.py @@ -76,7 +76,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/collect.shared.xml --- a/mothur/tools/mothur/collect.shared.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/collect.shared.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Generate collector's curves for calculators on OTUs mothur_wrapper.py @@ -76,8 +76,10 @@ - + + + @@ -85,7 +87,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/collect.single.xml --- a/mothur/tools/mothur/collect.single.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/collect.single.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Generate collector's curves for OTUs mothur_wrapper.py @@ -79,7 +79,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/consensus.seqs.xml --- a/mothur/tools/mothur/consensus.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/consensus.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Find a consensus sequence for each OTU or phylotype mothur_wrapper.py @@ -22,6 +22,9 @@ #else --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.cons\.summary$:'$summary,'^\S+\.cons\.fasta$:'$cons_fasta #end if +#if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count +#end if @@ -45,6 +48,7 @@ For example: cutoff=95 would return the base that was supported by at least 95% of sequences. + @@ -56,7 +60,7 @@ - mothur +mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/cooccurrence.xml --- a/mothur/tools/mothur/cooccurrence.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/cooccurrence.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + tests whether presence-absence patterns differ from chance mothur_wrapper.py @@ -61,7 +61,7 @@ - mothur + mothur @@ -140,5 +140,7 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _cooccurrence: http://www.mothur.org/wiki/Cooccurrence +v1.26.0: Updated to Mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/corr.axes.xml --- a/mothur/tools/mothur/corr.axes.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/corr.axes.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + correlation of data to axes mothur_wrapper.py @@ -65,7 +65,7 @@ - mothur + mothur @@ -84,6 +84,8 @@ .. _corr.axes: http://www.mothur.org/wiki/Corr.axes +v.1.21.0: Updated to mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/count.groups.xml --- a/mothur/tools/mothur/count.groups.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/count.groups.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,9 +1,9 @@ - + counts the number of sequences represented by a specific group or set of groups mothur_wrapper.py --cmd='count.groups' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.groups.count$:'$grp_count + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.groups.count$:'$grp_count,'^\S+\.summary$: '$summary --outputdir='$logfile.extra_files_path' #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): --shared=$group @@ -47,9 +47,10 @@ + - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/count.seqs.xml --- a/mothur/tools/mothur/count.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/count.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + (aka make.table) counts the number of sequences represented by the representative mothur_wrapper.py @@ -38,7 +38,7 @@ - mothur + mothur @@ -60,5 +60,7 @@ .. _count.seqs: http://www.mothur.org/wiki/Count.seqs .. _count_table: http://www.mothur.org/wiki/Count_File +v.1.21.0: Updated to Mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/create.database.xml --- a/mothur/tools/mothur/create.database.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/create.database.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + creates a database file from a list, repnames, repfasta and contaxonomy file mothur_wrapper.py @@ -28,6 +28,7 @@ help="fasta file output by get.oturep"/> + @@ -42,7 +43,7 @@ - mothur + mothur @@ -63,6 +64,8 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _create.database: http://www.mothur.org/wiki/Create.database +v.1.28.0: Updated to Mothur 1.33, added count paramter. + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/degap.seqs.xml --- a/mothur/tools/mothur/degap.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/degap.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Remove gap characters from sequences mothur_wrapper.py @@ -15,7 +15,7 @@ - mothur + mothur @@ -34,6 +34,8 @@ .. _degap.seqs: http://www.mothur.org/wiki/Degap.seqs +v1.21.0: Updated to Mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/deunique.seqs.xml --- a/mothur/tools/mothur/deunique.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/deunique.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,23 +1,30 @@ - + Return all sequences mothur_wrapper.py --cmd='deunique.seqs' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.redundant\.fasta$:'$out_fasta + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.redundant\.fasta$:'$out_fasta,'^\S+\.groups$:'$groups_file --outputdir='$logfile.extra_files_path' - --fasta=$fasta - --name=$names + --fasta=$fasta + #if isinstance($names.datatype, $__app__.datatypes_registry.get_datatype_by_extension('count_table').__class__): + --count=$names + #else + --name=$names + #end if - + - + + + (isinstance($names.datatype, $__app__.datatypes_registry.get_datatype_by_extension('count_table').__class__)) + - mothur + mothur @@ -37,6 +44,8 @@ .. _name: http://www.mothur.org/wiki/Name_file .. _deunique.seqs: http://www.mothur.org/wiki/Deunique.seqs +v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/deunique.tree.xml --- a/mothur/tools/mothur/deunique.tree.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/deunique.tree.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Reinsert the redundant sequence identiers back into a unique tree. mothur_wrapper.py @@ -17,7 +17,7 @@ - mothur + mothur @@ -37,6 +37,8 @@ .. _name: http://www.mothur.org/wiki/Name_file .. _deunique.tree: http://www.mothur.org/wiki/Deunique.tree +v1.21.0: Updated to Mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/dist.seqs.xml --- a/mothur/tools/mothur/dist.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/dist.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + calculate uncorrected pairwise distances between aligned sequences mothur_wrapper.py @@ -49,7 +49,7 @@ - mothur + mothur @@ -70,6 +70,8 @@ .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _dist.seqs: http://www.mothur.org/wiki/Dist.seqs +v.1.20.0: Updated to Mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/dist.shared.xml --- a/mothur/tools/mothur/dist.shared.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/dist.shared.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Generate a phylip-formatted dissimilarity distance matrix among multiple groups mothur_wrapper.py @@ -112,13 +112,13 @@ - + - mothur + mothur @@ -139,6 +139,8 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _dist.shared: http://www.mothur.org/wiki/Dist.shared +v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available. + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/fastq.info.xml --- a/mothur/tools/mothur/fastq.info.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/fastq.info.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Convert fastq to fasta and quality mothur_wrapper.py @@ -6,11 +6,74 @@ --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fasta$:'$out_fasta,'^\S+\.qual$:'$out_qfile --outputdir='$logfile.extra_files_path' --fastq=$fastq + --pacbio=$pacbio + --format=$format + + #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 + #if $oligo.ldiffs.__str__ != '' and int($oligo.ldiffs.__str__) > 0: + --ldiffs=$oligo.ldiffs + #end if + #if $oligo.sdiffs.__str__ != '' and int($oligo.sdiffs.__str__) > 0: + --sdiffs=$oligo.sdiffs + #end if + --datasetid='$fastq.info.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.(\S+\.flow)$:sff.flow' + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -22,7 +85,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/filter.seqs.xml --- a/mothur/tools/mothur/filter.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/filter.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + removes columns from alignments mothur_wrapper.py @@ -57,7 +57,7 @@ - mothur + mothur @@ -76,6 +76,8 @@ .. _filter.seqs: http://www.mothur.org/wiki/Filter.seqs +v.1.20.0: Updated to Mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/get.coremicrobiome.xml --- a/mothur/tools/mothur/get.coremicrobiome.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.coremicrobiome.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + fraction of OTUs for samples or abundances mothur_wrapper.py @@ -58,7 +58,7 @@ - mothur + mothur @@ -77,6 +77,8 @@ .. _get.coremicrobiome: http://www.mothur.org/wiki/Get.coremicrobiome +v1.27.0: Updated to Mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/get.group.xml --- a/mothur/tools/mothur/get.group.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.group.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + group names from shared or from list and group mothur_wrapper.py @@ -15,7 +15,7 @@ - mothur + mothur @@ -34,5 +34,7 @@ .. _get.group: http://www.mothur.org/wiki/Get.group +v.1.20.0: Updated to Mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/get.groups.xml --- a/mothur/tools/mothur/get.groups.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.groups.xml Fri Oct 31 15:09:32 2014 -0400 @@ -8,7 +8,11 @@ #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] --cmd='get.groups' --outputdir='$logfile.extra_files_path' - --group=$group_in + #if isinstance($group_in.datatype, $__app__.datatypes_registry.get_datatype_by_extension('groups').__class__): + --group=$group_in + #else + --count=$group_in + #end if #if $groupnames.source == 'groups': #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: --groups=$groupnames.groups @@ -45,7 +49,7 @@ --result=#echo ','.join($results) - + @@ -94,7 +98,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/get.lineage.xml --- a/mothur/tools/mothur/get.lineage.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.lineage.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,14 +1,21 @@ - + Picks by taxon mothur_wrapper.py #import re, os.path #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] ## adds .pick before the last extension to the input file - #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__] --cmd='get.lineage' + #if $file.filetype.__str__ == "usetaxonomy" + --taxonomy=$file.taxonomy + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__] + #else + --constaxonomy=$file.constaxonomy + --shared=$file.shared + --list=$file.list + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy.__str__)) + ":'" + $taxonomy_out.__str__] + #end if --outputdir='$logfile.extra_files_path' - --taxonomy=$taxonomy --taxon="'$re.sub('(\s|,)+',',',$re.sub('\(\d+\)','',$taxon.value.__str__))'" #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: --fasta=$fasta_in @@ -30,11 +37,28 @@ --name=$name_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] $dups - #end if + #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if --result=#echo ','.join($results) - + + + + + + + + + + + + + + + @@ -85,12 +91,17 @@ + + + + + - mothur +mothur @@ -109,5 +120,7 @@ .. _get.oturep: http://www.mothur.org/wiki/Get.oturep +v1.23.0: Updated to Mothur 1.33, added count and method parameter + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/get.otus.xml --- a/mothur/tools/mothur/get.otus.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.otus.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Get otus containing sequences from specified groups mothur_wrapper.py @@ -55,7 +55,7 @@ - mothur + mothur @@ -75,6 +75,7 @@ .. _list: http://www.mothur.org/wiki/List_file .. _get.otus: http://www.mothur.org/wiki/Get.otus +v.1.20.0: Updated to Mothur 1.33 diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/get.rabund.xml --- a/mothur/tools/mothur/get.rabund.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.rabund.xml Fri Oct 31 15:09:32 2014 -0400 @@ -14,6 +14,9 @@ --label=$label #end if $sorted + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if @@ -24,13 +27,14 @@ + - mothur +mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/get.relabund.xml --- a/mothur/tools/mothur/get.relabund.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.relabund.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Calculate the relative abundance of each otu mothur_wrapper.py @@ -42,7 +42,7 @@ - mothur + mothur @@ -62,5 +62,6 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _get.relabund: http://www.mothur.org/wiki/Get.relabund +v.1.21.0: Updated to Mothur 1.33 diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/get.sabund.xml --- a/mothur/tools/mothur/get.sabund.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.sabund.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,54 +1,59 @@ - - Get sabund from a otu list or rabund - - mothur_wrapper.py - --cmd='get.sabund' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund - --outputdir='$logfile.extra_files_path' - #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): - --list=$otu - #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): - --rabund=$otu - #end if - #if $label.__str__ != "None" and len($label.__str__) > 0: - --label=$label - #end if - - - - - - - - - - - - - - - mothur - - - - -**Mothur Overview** + + Get sabund from a otu list or rabund + + mothur_wrapper.py + --cmd='get.sabund' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund + --outputdir='$logfile.extra_files_path' + #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): + --list=$otu + #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): + --rabund=$otu + #end if + #if $label.__str__ != "None" and len($label.__str__) > 0: + --label=$label + #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + + + + + + + + + -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 + + + + + + + mothur + + + + + **Mothur Overview** -**Command Documenation** + 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. -The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file. + .. _Mothur: http://www.mothur.org/wiki/Main_Page -.. _sabund: http://www.mothur.org/wiki/Sabund_file -.. _list: http://www.mothur.org/wiki/List_file -.. _rabund: http://www.mothur.org/wiki/Rabund_file -.. _get.sabund: http://www.mothur.org/wiki/Get.sabund + **Command Documenation** + + The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file. + + .. _sabund: http://www.mothur.org/wiki/Sabund_file + .. _list: http://www.mothur.org/wiki/List_file + .. _rabund: http://www.mothur.org/wiki/Rabund_file + .. _get.sabund: http://www.mothur.org/wiki/Get.sabund - + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/get.seqs.xml --- a/mothur/tools/mothur/get.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -38,6 +38,12 @@ #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] #end if --result=#echo ','.join($results) + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + #if $fastq.__str__ != "None" and len($fastq.__str__) > 0: + --fastq=$fastq + #end if @@ -49,6 +55,8 @@ + + @@ -77,7 +85,7 @@ - mothur +mothur @@ -102,5 +110,7 @@ .. _list.seqs: http://www.mothur.org/wiki/list.seqs .. _get.seqs: http://www.mothur.org/wiki/Get.seqs +v.1.27.0 : Updated to Mothur 1.33, added count and fastq params + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/get.sharedseqs.xml --- a/mothur/tools/mothur/get.sharedseqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.sharedseqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Get shared sequences at each distance from list and group mothur_wrapper.py @@ -6,8 +6,12 @@ --cmd='get.sharedseqs' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' - --list=$list - --group=$group + #if isinstance($list.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): + --list=$list + --group=$group + #else + --shared=$list + #end if #set datasets = ["'^\S+?\.((unique|[0-9.]*)(\S+)\.shared.seqs)$:tabular'"] #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' @@ -35,8 +39,8 @@ #end if - - + + @@ -78,7 +82,7 @@ - mothur + mothur @@ -97,5 +101,7 @@ .. _get.sharedseqs: http://www.mothur.org/wiki/Get.sharedseqs +v1.21.0: Updated to Mothur 1.33, added shared file option + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/hcluster.xml --- a/mothur/tools/mothur/hcluster.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/hcluster.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Assign sequences to OTUs (Operational Taxonomic Unit) mothur_wrapper.py @@ -76,7 +76,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/heatmap.bin.xml --- a/mothur/tools/mothur/heatmap.bin.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/heatmap.bin.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Generate a heatmap for OTUs mothur_wrapper.py @@ -102,7 +102,7 @@ - mothur + mothur @@ -123,5 +123,6 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin +v.1.21.0: Updated to Mothur 1.33 diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/heatmap.sim.xml --- a/mothur/tools/mothur/heatmap.sim.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/heatmap.sim.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Generate a heatmap for pariwise similarity mothur_wrapper.py @@ -35,6 +35,9 @@ #if 100 > $fontsize > 0: --fontsize=$fontsize #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if @@ -78,6 +81,7 @@ + @@ -86,7 +90,7 @@ - mothur +mothur @@ -109,5 +113,6 @@ .. _name: http://www.mothur.org/wiki/Name_file .. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim +v.1.24.0: Updated to Mothur 1.33, added count parameter diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/homova.xml --- a/mothur/tools/mothur/homova.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/homova.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Homogeneity of molecular variance mothur_wrapper.py @@ -13,20 +13,28 @@ #if float($alpha.__str__) > 0.0: --alpha=$alpha #end if + #if $sets.__str__ != "None" and len ($sets.__str__) >0: + --sets=$sets + #end if - + + + + + + - mothur + mothur @@ -57,6 +65,7 @@ .. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _homova: http://www.mothur.org/wiki/Homova +v.1.20.0: Updated to Mothur 1.33, added sets parameter diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/indicator.xml --- a/mothur/tools/mothur/indicator.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/indicator.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Identify indicator "species" for nodes on a tree mothur_wrapper.py @@ -51,7 +51,7 @@ - mothur + mothur @@ -72,6 +72,7 @@ .. _relabund: http://www.mothur.org/wiki/Get.relabund .. _indicator: http://www.mothur.org/wiki/Indicator +v.1.22.0: Updated to Mothur 1.33 diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/libshuff.xml --- a/mothur/tools/mothur/libshuff.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/libshuff.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Cramer-von Mises tests communities for the same structure mothur_wrapper.py @@ -52,7 +52,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/list.otulabels.xml --- a/mothur/tools/mothur/list.otulabels.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/list.otulabels.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Lists otu labels from shared or relabund file mothur_wrapper.py @@ -8,7 +8,9 @@ #if isinstance($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 + --relabund=$otu + #else + --list=$otu #end if #if $label.__str__ != "None" and len($label.__str__) > 0: --label=$label @@ -18,7 +20,7 @@ #end if - + @@ -35,7 +37,7 @@ - mothur + mothur @@ -61,6 +63,7 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _relabund: http://www.mothur.org/wiki/Get.relabund +v.1.27.0: Updated to mothur 1.33, added list file for otu diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/list.seqs.xml --- a/mothur/tools/mothur/list.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/list.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Lists the names (accnos) of the sequences mothur_wrapper.py @@ -18,6 +18,9 @@ #elif $search.type == "taxonomy": --taxonomy=$search.input #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if @@ -48,6 +51,8 @@ + + @@ -55,7 +60,7 @@ - mothur +mothur @@ -79,6 +84,7 @@ .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline .. _list.seqs: http://www.mothur.org/wiki/list.seqs +v.1.20.0: Updated to mothur 1.33, added count and fastq option diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/make.biom.xml --- a/mothur/tools/mothur/make.biom.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.biom.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,72 +1,95 @@ - - Make biom files from a shared file - - mothur_wrapper.py - #import re, os.path - --cmd='make.biom' - --result='^mothur.\S+\.logfile$:'$logfile - --outputdir='$logfile.extra_files_path' - --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.((\S+)\.biom)$:biom' - --shared=$shared - #if $contaxonomy != 'none' and len($contaxonomy.__str__) > 0: - --contaxonomy=$contaxonomy - #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=$groups - #end if - --matrixtype=$matrixtype - - - - - - - - - - - - - - - - - - - - - - - - mothur - - - - -**Mothur Overview** + + Make biom files from a shared file + + mothur_wrapper.py + #import re, os.path + --cmd='make.biom' + --result='^mothur.\S+\.logfile$:'$logfile + --outputdir='$logfile.extra_files_path' + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.((\S+)\.biom)$:biom' + --shared=$shared + #if $contaxonomy.__str__ != 'None' and len($contaxonomy.__str__) > 0: + --constaxonomy=$contaxonomy + #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=$groups + #end if + --matrixtype=$matrixtype + #if $metadata.__str__ != 'None' and len($metadata.__str__) > 0: + --metadata=$metadata + #end if + #if $picrustc.use: + #if $picrustc.picrust.__str__ != '': + --picrust=$picrustc.picrust + #end if + #if $picrustc.reftax.__str__ != '': + --reftaxonomy=$picrustc.reftax + #end if + #end if + + + + + + + + + + + + + -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 + + + + + **Mothur Overview** -.. _Mothur: http://www.mothur.org/wiki/Main_Page + 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. -**Command Documenation** + .. _Mothur: http://www.mothur.org/wiki/Main_Page -The make.biom command converts a shared_ shared file to biom_ files. -The output can be filtered by groups and labels. + **Command Documenation** + + The make.biom command converts a shared_ shared file to biom_ files. + The output can be filtered by groups and labels. -.. _shared: http://www.mothur.org/wiki/Shared_file -.. _biom: http://biom-format.org/documentation/biom_format.html -.. _make.biom: http://www.mothur.org/wiki/Make.biom + .. _shared: http://www.mothur.org/wiki/Shared_file + .. _biom: http://biom-format.org/documentation/biom_format.html + .. _make.biom: http://www.mothur.org/wiki/Make.biom - + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/make.contigs.xml --- a/mothur/tools/mothur/make.contigs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.contigs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Aligns paired forward and reverse fastq files to contigs as fasta and quality mothur_wrapper.py @@ -19,6 +19,12 @@ #if $oligo.tdiffs.__str__ != '' and int($oligo.tdiffs.__str__) > 0: --tdiffs=$oligo.tdiffs #end if + #if $oligo.findex.__str__ != 'None': + --findex=$oligo.findex + #end if + #if $oligo.rindex.__str__ != 'None': + --rindex=$oligo.rindex + #end if #end if #if $match.__str__ != '': @@ -65,6 +71,8 @@ + + @@ -85,7 +93,7 @@ - mothur + mothur @@ -104,5 +112,7 @@ .. _make.contigs: http://www.mothur.org/wiki/Make.contigs +v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file. + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/make.design.xml --- a/mothur/tools/mothur/make.design.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.design.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Assign groups to Sets cat $generated_design > $design @@ -29,7 +29,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/make.fastq.xml --- a/mothur/tools/mothur/make.fastq.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.fastq.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,48 +1,65 @@ - - Convert fasta and quality to fastq - - mothur_wrapper.py - --cmd='make.fastq' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq - --outputdir='$logfile.extra_files_path' - --fasta=$fasta - --qfile=$qfile - - - - - - - - - - - - - - - - - - mothur - - - - -**Mothur Overview** + + Convert fasta and quality to fastq + + mothur_wrapper.py + --cmd='make.fastq' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq + --outputdir='$logfile.extra_files_path' + --fasta=$fasta + --qfile=$qfile + #if $chooseformat.use: + --format=$chooseformat.format + #end if + + + + + + + -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 + + + + + **Mothur Overview** -.. _Mothur: http://www.mothur.org/wiki/Main_Page + 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. -**Command Documenation** + .. _Mothur: http://www.mothur.org/wiki/Main_Page -The fastq.info_ command reads a fasta file and quality file and creates a fastq. + **Command Documenation** + + The fastq.info_ command reads a fasta file and quality file and creates a fastq. -.. _fastq.info: http://www.mothur.org/wiki/Make.fastq + .. _fastq.info: http://www.mothur.org/wiki/Make.fastq - + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/make.group.xml --- a/mothur/tools/mothur/make.group.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.group.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Make a group file mothur_wrapper.py @@ -21,7 +21,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/make.shared.xml --- a/mothur/tools/mothur/make.shared.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.shared.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Make a shared file from a list and a group mothur_wrapper.py @@ -10,8 +10,14 @@ --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund' #end if - --list=$list - --group=$group + --list=$list + + #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('groups').__class__): + --group=$group + #else: + --count=$group + #end if + #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if @@ -26,7 +32,7 @@ - + @@ -48,7 +54,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/mantel.xml --- a/mothur/tools/mothur/mantel.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/mantel.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Mantel correlation coefficient between two matrices. mothur_wrapper.py @@ -27,7 +27,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/merge.files.xml --- a/mothur/tools/mothur/merge.files.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/merge.files.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Merge data mothur_wrapper.py @@ -54,7 +54,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/merge.groups.xml --- a/mothur/tools/mothur/merge.groups.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/merge.groups.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + Merge groups in a shared file mothur_wrapper.py @@ -85,7 +85,7 @@ - mothur + mothur diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/merge.sfffiles.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/merge.sfffiles.xml Fri Oct 31 15:09:32 2014 -0400 @@ -0,0 +1,45 @@ + + Merge SFF files + + mothur_wrapper.py + --cmd='merge.sfffiles' + --result='^mothur.\S+\.logfile$:'$logfile,'mergefile:'$output + --outputdir='$logfile.extra_files_path' + --sff=${input}#for i in $inputs#,${i.input}#end for# + --output='mergefile' + + + + + + + + + + + + + + + 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.sfffiles_ command merge inputs into a single output. + +.. _merge.sfffiles: http://www.mothur.org/wiki/Merge.sfffiles + + + + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/metastats.xml --- a/mothur/tools/mothur/metastats.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/metastats.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ - + generate principle components plot data mothur_wrapper.py @@ -55,7 +55,7 @@ - mothur + mothur @@ -74,5 +74,7 @@ .. _metastats: http://www.mothur.org/wiki/Metastats +v.1.21.0: Updated to mothur 1.33 + diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/mothur_wrapper.py --- a/mothur/tools/mothur/mothur_wrapper.py Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/mothur_wrapper.py Fri Oct 31 15:09:32 2014 -0400 @@ -44,8 +44,8 @@ assert sys.version_info[:2] >= ( 2, 4 ) -debug = False -#debug = True +#debug = False +debug = True max_processors = os.getenv('MOTHUR_MAX_PROCESSORS') if os.getenv('MOTHUR_MAX_PROCESSORS') else 8 def stop_err( msg ): @@ -53,6 +53,7 @@ sys.exit() def __main__(): + global debug # tranform the logfile into html # add extra file ouput # add object tags for svg files @@ -67,15 +68,15 @@ html.write("%s\n\n
\n" % title)
         try:
             for line in txt:
-		if line.find('set.dir') >= 0:
+                if line.find('set.dir') >= 0:
                     continue
-		elif line.find('put directory to ') >= 0:
+                elif line.find('put directory to ') >= 0:
                     continue
-		elif line.startswith('Mothur\'s directories:') :
+                elif line.startswith('Mothur\'s directories:') :
                     continue
-		elif line.startswith('outputDir=') :
+                elif line.startswith('outputDir=') :
                     continue
-		elif line.startswith('Type ') :
+                elif line.startswith('Type ') :
                     continue
                 elif line.find(tmp_output_dir_name) >= 0:
                     # if debug:  print >> sys.stdout, 'logfile_to_html #%s#' % line
@@ -119,7 +120,7 @@
                     except:
                         shutil.copy(val,os.path.join(input_dir,fname))
                     vals.append(fname)
-                    if debug: print >> sys.stderr, "scp %s %s" % (val, os.path.join(input_dir,fname))
+                    if debug: print >> sys.stdout, "scp %s %s" % (val, os.path.join(input_dir,fname))
                 else:
                     vals.append(convert_value(val))
             return '-'.join(vals)
@@ -164,10 +165,10 @@
         Gather parameter values for the specified mothur command 'cmd',
         using the definition from the 'cmd_dict' dictionary.
         """
-        if debug: print >> sys.stderr, options
+        if debug: print >> sys.stdout, options
         params = []  
         for opt in cmd_dict[cmd]['required']:
-            if debug: print >> sys.stderr, opt
+            if debug: print >> sys.stdout, opt
             if isinstance(opt,list): # One of these must be present
                 missing = True
                 for sel in opt:
@@ -212,33 +213,33 @@
     The complexity of inputs should be handled by the glaxy tool xml file.
     """
     cmd_dict = dict()
-    cmd_dict['align.check'] = dict({'required' : ['fasta','map']})
+    cmd_dict['align.check'] = dict({'required' : ['fasta','map'], 'optional' : ['name','count']})
     cmd_dict['align.seqs'] = dict({'required' : ['fasta','reference',], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','save','processors']})
-    cmd_dict['amova'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
+    cmd_dict['amova'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters','sets']})
     cmd_dict['anosim'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
-    cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group']})
+    cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group','count']})
     cmd_dict['bootstrap.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','groups','iters','label']})
     #catchall
     cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']})
     cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','save','processors']})
     cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','save','processors']})
-    cmd_dict['chimera.perseus'] = dict({'required' : ['fasta','name'], 'optional' : ['group','alpha','beta','cutoff']})
+    cmd_dict['chimera.perseus'] = dict({'required' : ['fasta',['name','count']], 'optional' : ['group','alpha','beta','cutoff','dereplicate']})
     cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','save','processors']})
-    cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','reference'], 'optional' : ['name','group','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','blastlocation','save','processors']})
-    cmd_dict['chimera.uchime'] = dict({'required' : ['fasta'], 'optional' : ['name','group','reference','abskew','chimealns','minh','mindiv','xn','dn','xa','chunks','minchunk','idsmoothwindow','minsmoothid','maxp','skipgaps','skipgaps2','minlen','maxlen','ucl','queryfract','processors']})
-    cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'],  'optional' : ['countgaps','keep','short']})
-    cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']})
-    cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','save','processors']})
+    cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','reference'], 'optional' : ['name','group','count','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','blastlocation','save','processors','dereplicate']})
+    cmd_dict['chimera.uchime'] = dict({'required' : ['fasta'], 'optional' : ['name','group','count','dereplicate','reference','abskew','chimealns','minh','mindiv','xn','dn','xa','chunks','minchunk','idsmoothwindow','minsmoothid','maxp','skipgaps','skipgaps2','minlen','maxlen','ucl','queryfract','processors']})
+    cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'],  'optional' : ['countgaps','keep','short','name','group','count']})
+    cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy','count','persample']})
+    cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','save','processors','count','relabund']})
     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','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','count','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','classic','timing','processors']})
+    cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] ,  'optional' : ['name','diffs','percent','count']})
+    cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] ,  'optional' : ['name','count','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','classic','timing','processors','cluster']})
     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']})
+    cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label','cutoff','count']})
 
     cmd_dict['cooccurrence'] = dict({'required' : ['shared'], 'optional' : ['iters','metric','matrixmodel','groups','label']})
 
@@ -246,40 +247,40 @@
     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','shared'],'repfasta','repname','contaxonomy'], 'optional' : ['group','label']})
+    cmd_dict['create.database'] = dict({'required' : [['list','shared'],'repfasta','repname','constaxonomy','count'], 'optional' : ['group','label']})
 
     cmd_dict['degap.seqs'] = dict({'required' : ['fasta']})
-    cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'],  'optional' : []})
+    cmd_dict['deunique.seqs'] = dict({'required' : ['fasta'],  'optional' : ['name','count']})
     cmd_dict['deunique.tree'] = dict({'required' : ['tree','name'],  'optional' : []})
     cmd_dict['dist.seqs'] = dict({'required' : ['fasta'],  'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']})
     cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output','subsample','iters','processors']})
-    cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : ['fasta','qfile']})
+    cmd_dict['fastq.info'] = dict({'required' : ['fastq','format'], 'optional' : ['fasta','qfile','pacbio','oligos','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs']})
     cmd_dict['filter.seqs'] = dict({'required' : ['fasta'],  'optional' : ['vertical','trump','soft','hard','processors']})
     cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []})
     cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy','design']})
     cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
     cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']})
-    cmd_dict['get.oturep'] = dict({'required' : ['list',['phylip','column']], 'optional' : ['fasta','name','label','group','groups','sorted','precision','cutoff','large','weighted']})
+    cmd_dict['get.oturep'] = dict({'required' : ['list',['phylip','column']], 'optional' : ['fasta','name','label','group','groups','sorted','precision','cutoff','large','weighted','count','method']})
     cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
-    cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']})
+    cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label','count']})
     cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']})
-    cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label']})
-    cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
-    cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']})
+    cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label','count']})
+    cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups','count','fastq']})
+    cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta','shared']})
     cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']})
     cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
-    cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups','fontsize']})
-    cmd_dict['homova'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
+    cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups','fontsize','count']})
+    cmd_dict['homova'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters','sets']})
     cmd_dict['indicator'] = dict({'required' : [['tree','design'],['shared','relabund']], 'optional' : ['groups','label','processors']})
     cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']})
     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['list.otulabels'] = dict({'required': [['shared','relabund','list']], 'optional': ['group','label']})
+    cmd_dict['make.biom'] = dict({'required' : ['shared'] ,  'optional' : ['constaxonomy','matrixtype','groups','label','metadata','picrust','reftaxonomy']})
+    cmd_dict['make.contigs'] = dict({'required' : ['ffastq','rfastq',], 'optional' : ['align','match','mismatch','gapopen','gapextend','threshold','oligos','bdiffs','pdiffs','tdiffs','processors','rindex','findex']})
 
-    cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] ,  'optional' : []})
+    cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] ,  'optional' : ['format']})
     cmd_dict['make.group'] = dict({'required' : ['fasta','groups'],  'optional' : []})
-    cmd_dict['make.shared'] = dict({'required' : [['list','group','biom']],  'optional' : ['label','groups']})
+    cmd_dict['make.shared'] = dict({'required' : [['list','group','biom','count']],  'optional' : ['label','groups']})
     cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] ,  'optional' : ['method','iters']})
     cmd_dict['merge.files'] = dict({'required' : ['input','output']})
     cmd_dict['merge.groups'] = dict({'required' : [['shared','group'],'design'],  'optional' : ['groups', 'label']})
@@ -289,46 +290,48 @@
     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']})
-    cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']})
+    cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label','count']})
+    cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors','count']})
     cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']})
     cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']})
 
-    cmd_dict['pcr.seqs'] = dict({'required' : ['fasta'], 'optional' : ['oligos','name','group','taxonomy','ecoli','start','end','nomatch','keepprimer','keepdots','processors']})
+    cmd_dict['pcr.seqs'] = dict({'required' : ['fasta'], 'optional' : ['oligos','name','group','taxonomy','ecoli','start','end','nomatch','keepprimer','keepdots','processors','count','pdiffs']})
 
-    cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']})
+    cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors','count']})
     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','design','sets','groupmode']})
+    cmd_dict['pre.cluster'] = dict({'required' : ['fasta'],  'optional' : ['name','count','diffs','group','processors','topdown']})
+    cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble','design','sets','groupmode','subsample','subsampleiters']})
     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']})
+    cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy','design','count']})
+    cmd_dict['remove.lineage'] = dict({'required' : [['taxonomy','constaxonomy'],'taxon'],'optional' : ['fasta','name','group','list','alignreport','dups','shared','list','count']})
     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['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
+    cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup','count']})
+    cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups','count','fastq']})
     cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']})
-    cmd_dict['screen.seqs'] = dict({'required' : ['fasta'],  'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','taxonomy','processors']})
+    cmd_dict['screen.seqs'] = dict({'required' : ['fasta'],  'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','taxonomy','processors','count','summary','contigsreport']})
     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['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['oligos','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','fasta','qfile','trim','sfftxt','flow','accnos']})
     cmd_dict['shhh.flows'] = dict({'required' : [['flow']], 'optional' : ['lookup','maxiter','mindelta','cutoff','sigma','order','large','processors']})
     cmd_dict['shhh.seqs'] = dict({'required' : [['fasta','name']], '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']})
-    cmd_dict['sort.seqs'] = dict({'required' : [['fasta','qfile','name','group','flow','taxonomy']], 'optional' : ['accnos','large']})
-    cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']})
-    cmd_dict['summary.qual'] = dict({'required' : ['qfile'], 'optional' : ['name']})
-    cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']})
-    cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']})
-    cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']})
-    cmd_dict['summary.tax'] = dict({'required' : ['taxonomy'], 'optional' : ['name','group','reftaxonomy']})
-    cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label','subsample','iters','processors']})
+    cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list','count']], 'optional' : ['cutoff','group','groups','label','accnos']})
+    cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups','count']})
+    cmd_dict['sort.seqs'] = dict({'required' : [['fasta','qfile','name','group','flow','taxonomy']], 'optional' : ['accnos','large','count']})
+    cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample','count','taxonomy']})
+    cmd_dict['summary.qual'] = dict({'required' : ['qfile'], 'optional' : ['name','count']})
+    cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors','count']})
+    cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors','subsample','iters']})
+    cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode','subsample','iters']})
+    cmd_dict['summary.tax'] = dict({'required' : ['taxonomy'], 'optional' : ['name','group','reftaxonomy','count','relabund']})
+    cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label','subsample','iters','processors','count']})
     cmd_dict['trim.flows'] = dict({'required' : ['flow'],  'optional' : ['oligos','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','minflows','maxflows','fasta','signal','noise','maxhomop','order','processors']})
-    cmd_dict['trim.seqs'] = dict({'required' : ['fasta'],  'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','keepforward','allfiles','keepfirst','removelast','processors']})
-    cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors']})
-    cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors']})
-    cmd_dict['unique.seqs'] = dict({'required' : ['fasta'],  'optional' : ['name']})
-    cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute','fontsize']})
+    cmd_dict['trim.seqs'] = dict({'required' : ['fasta'],  'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','keepforward','allfiles','keepfirst','removelast','processors','count','checkorient','logtransform']})
+    cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors','count']})
+    cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors','count']})
+    cmd_dict['unique.seqs'] = dict({'required' : ['fasta'],  'optional' : ['name','count']})
+    cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute','fontsize','sharedotus']})
+
+    cmd_dict['merge.sfffiles'] = dict({'required' : ['sff','output']})
 
     parser = optparse.OptionParser()
     # Options for managing galaxy interaction
@@ -405,7 +408,7 @@
     parser.add_option( '--report', dest='report', help='' )
     parser.add_option( '--taxonomy', dest='taxonomy', help='A Taxonomy file' )
     parser.add_option( '--reftaxonomy', dest='reftaxonomy', help='A Taxonomy file' )
-    parser.add_option( '--contaxonomy', dest='contaxonomy', help='The Taxonomy file output by classify.otu' )
+    parser.add_option( '--constaxonomy', dest='constaxonomy', help='The Taxonomy file output by classify.otu' )
     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' )
@@ -532,6 +535,7 @@
     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' )
+    parser.add_option( '--dereplicate', dest='dereplicate', help='Boolean - remove chimeric sequences from all groups, default=f')
     parser.add_option( '--abskew', dest='abskew', type="float", help='Minimum abundance skew.')
     parser.add_option( '--chimealns', dest='chimealns', help='Boolean - produce a file containing multiple alignments of query sequences')
     parser.add_option( '--minh', dest='minh', type="float", help='mininum score to report chimera.')
@@ -568,11 +572,20 @@
     # include read.tree options
     parser.add_option( '--tree', dest='tree', help='' )
 
+    # trim.seq options
+    parser.add_option( '--checkorient', dest='checkorient', help='' )
+    parser.add_option( '--logtransform', dest='logtransform', help='' )
+    #fastq.info options
+    parser.add_option( '--format', dest='format', help='' )
+    parser.add_option( '--pacbio', dest='pacbio', help='' )
+    parser.add_option( '--picrust', dest='picrust', help='' )
+    parser.add_option( '--subsampleiters', dest='subsampleiters', help='' )
+
     (options, args) = parser.parse_args()
     """
     """
     # print >> sys.stderr, options # so will appear as blurb for file
-    if options.debug != None:
+    if debug == None and options.debug != None:
        debug = options.debug
     params = []  
     inputdir = None
@@ -658,20 +671,26 @@
         tmp_stderr.close()
         tmp_stdout.close()
         if debug: print >> sys.stdout, 'parse %s' % tmp_stdout_name
+        
         if returncode != 0:
-            try:
-                # try to copy stdout to the logfile
-                for output in options.result.split(','):
-                    # Each item has a regex pattern and a file path to a galaxy dataset
-                    (pattern,path) = output.split(':')
-                    if debug: print >> sys.stdout, '%s -> %s' % (pattern,path)
-                    if pattern.find('\.logfile') > 0: 
-                        if path != None and os.path.exists(path):
-                            logfile_to_html(tmp_stdout_name,path,inputdir,outputdir,title="Mothur %s Error Logfile" % options.cmd)
-                        break
-            except:
-                pass
-            raise Exception, stderr
+            if returncode == -11 and options.cmd == 'seq.error':
+                if debug: print >> sys.stdout, 'seq.error produced a segmentation fault but we are ignoring it.'
+            else: 
+                try:
+                    # try to copy stdout to the logfile
+                    for output in options.result.split(','):
+                        # Each item has a regex pattern and a file path to a galaxy dataset
+                        (pattern,path) = output.split(':')
+                        if debug: print >> sys.stdout, '%s -> %s' % (pattern,path)
+                        if pattern.find('\.logfile') > 0: 
+                            if path != None and os.path.exists(path):
+                                logfile_to_html(tmp_stdout_name,path,inputdir,outputdir,title="Mothur %s Error Logfile" % options.cmd)
+                            break
+                except:
+                    pass
+                
+                raise Exception, stderr + "  Return code: " + str(returncode)
+            
         stdout = ''
         # Parse stdout to provide info
         tmp_stdout = open( tmp_stdout_name, 'rb' )
@@ -713,7 +732,7 @@
                     continue
                 if line.find(outputdir) >= 0:
                     continue
-	        if line.startswith('**************'):
+                if line.startswith('**************'):
                     continue
                 if re.match('^Processing.*',line):
                     continue
@@ -733,7 +752,7 @@
                     continue
                 if re.match('Output .*',line):
                     break
-		if re.match('mothur > quit()',line):
+                if re.match('mothur > quit()',line):
                     break
                 if found_begin and info_chars < 200:
                     info += "%s" % line
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/nmds.xml
--- a/mothur/tools/mothur/nmds.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/nmds.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  generate non-metric multidimensional scaling data
  
   mothur_wrapper.py 
@@ -41,7 +41,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
@@ -61,6 +61,7 @@
 .. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
 .. _nmds: http://www.mothur.org/wiki/Nmds
 
+v1.20.0: Updated to mothur 1.33
 
  
 
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/normalize.shared.xml
--- a/mothur/tools/mothur/normalize.shared.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/normalize.shared.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Normalize the number of sequences per group to a specified level
  
   mothur_wrapper.py 
@@ -50,7 +50,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/otu.association.xml
--- a/mothur/tools/mothur/otu.association.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/otu.association.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Calculate the correlation coefficient for the otus
  
   mothur_wrapper.py 
@@ -24,6 +24,10 @@
   #if $metadata.__str__ != "None" and len($method.__str__) > 0:
    --metadata=$metadata
   #end if
+	#if $cutoff.__str__ != '':
+   --cutoff=$cutoff
+  #end if
+  
  
  
   
@@ -43,12 +47,13 @@
    
   
   
+  
  
  
   
  
  
-  mothur
+  mothur
  
  
  
@@ -69,5 +74,7 @@
 .. _relabund: http://www.mothur.org/wiki/Get.relabund
 .. _otu.association: http://www.mothur.org/wiki/Otu.association
 
+v.1.25.0: Updated to mothur 1.33, added cutoff option
+
  
 
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/otu.hierarchy.xml
--- a/mothur/tools/mothur/otu.hierarchy.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/otu.hierarchy.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Relate OTUs at different distances
  
   mothur_wrapper.py 
@@ -33,7 +33,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/pairwise.seqs.xml
--- a/mothur/tools/mothur/pairwise.seqs.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/pairwise.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  calculate uncorrected pairwise distances between sequences
  
   mothur_wrapper.py 
@@ -74,7 +74,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/parse.list.xml
--- a/mothur/tools/mothur/parse.list.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/parse.list.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -12,6 +12,9 @@
   #if $label.__str__ != "None" and len($label.__str__) > 0:
    --label='$label'
   #end if
+	#if $count.__str__ != "None" and len($count.__str__) > 0:
+		--count=$count
+	#end if
  
  
   
@@ -22,12 +25,13 @@
     
    
   
+	
  
  
   
  
  
-  mothur
+mothur
  
  
  
@@ -48,5 +52,7 @@
 .. _group: http://www.mothur.org/wiki/Group_file
 .. _parse.list: http://www.mothur.org/wiki/Parse.list
 
+v.1.19.0: Updated to mothur 1.33, added count parameter
+
  
 
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/parsimony.xml
--- a/mothur/tools/mothur/parsimony.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/parsimony.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Describes whether two or more communities have the same structure
  
   mothur_wrapper.py 
@@ -19,6 +19,9 @@
    --iters=$iters
   #end if
   --processors=8
+	#if $count.__str__ != "None" and len($count.__str__) > 0:
+		--count=$count
+	#end if
  
  
   
@@ -34,6 +37,7 @@
   
+
  
  
   
@@ -47,7 +51,7 @@
   -->
  
  
-  mothur
+mothur
  
  
  
@@ -66,6 +70,8 @@
 
 .. _parsimony: http://www.mothur.org/wiki/Parsimony
 
+v.1.20.0: Added count parameter
+
 
  
 
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/pca.xml
--- a/mothur/tools/mothur/pca.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/pca.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Principal Coordinate Analysis for a shared file
  
   mothur_wrapper.py 
@@ -40,7 +40,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/pcoa.xml
--- a/mothur/tools/mothur/pcoa.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/pcoa.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Principal Coordinate Analysis for a distance matrix
  
   mothur_wrapper.py 
@@ -18,7 +18,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/pcr.seqs.xml
--- a/mothur/tools/mothur/pcr.seqs.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/pcr.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Trim sequences
  
   mothur_wrapper.py 
@@ -39,6 +39,9 @@
   $keepdots
   --result=#echo ','.join($results)
   --processors=8
+  #if $pdiffs.__str__ != '' and int($pdiffs.__str__) > 0:
+   --pdiffs=$pdiffs
+  #end if
  
  
   
@@ -81,7 +84,9 @@
   
   
   
-
+ 
+      
+    
  
  
   
@@ -99,7 +104,7 @@
 
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/phylo.diversity.xml
--- a/mothur/tools/mothur/phylo.diversity.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/phylo.diversity.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Alpha Diversity calculates unique branch length
  
   mothur_wrapper.py 
@@ -30,6 +30,9 @@
    $summary
   #end if
   --processors=8
+	#if $count.__str__ != "None" and len($count.__str__) > 0:
+		--count=$count
+	#end if
  
  
   
@@ -56,6 +59,7 @@
   
   
   
+	
  
  
   
@@ -74,7 +78,7 @@
   -->
  
  
-  mothur
+mothur
  
  
  
@@ -93,6 +97,8 @@
 
 .. _phylo.diversity: http://www.mothur.org/wiki/Phylo.diversity
 
+v.1.21.0: Updated to Mothur 1.33, added count parameter
+
 
  
 
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/phylotype.xml
--- a/mothur/tools/mothur/phylotype.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/phylotype.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Assign sequences to OTUs based on taxonomy
  
   mothur_wrapper.py 
@@ -41,7 +41,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/pre.cluster.xml
--- a/mothur/tools/mothur/pre.cluster.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/pre.cluster.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Remove sequences due to pyrosequencing errors
  
   mothur_wrapper.py 
@@ -10,10 +10,12 @@
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.precluster.map',$os.path.basename($fasta.__str__)) + ":'" + $map_out.__str__]
   --cmd='pre.cluster'
   --outputdir='$logfile.extra_files_path'
-  --fasta=$fasta
-  #if $name.__str__ != "None" and len($name.__str__) > 0:
+	--fasta=$fasta
+		#if isinstance($name.datatype, $__app__.datatypes_registry.get_datatype_by_extension('name').__class__):
    --name=$name
-  #end if
+ #else 
+ 	--count=$name
+ #end if
   #if $group.__str__ != "None" and len($group.__str__) > 0:
    --group=$group
   #end if
@@ -22,12 +24,14 @@
   #end if
   --result=#echo ','.join($results)
   --processors=8
+	--topdown
  
  
   
-  
+  
   
   
+
  
  
   
@@ -36,7 +40,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
@@ -55,6 +59,7 @@
 
 .. _pre.cluster: http://www.mothur.org/wiki/Pre.cluster
 
+v1.24.0: Updated to mothur 1.33, added count and topdown parameter
 
  
 
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/rarefaction.shared.xml
--- a/mothur/tools/mothur/rarefaction.shared.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/rarefaction.shared.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Generate inter-sample rarefaction curves for OTUs
  
   mothur_wrapper.py 
@@ -12,20 +12,20 @@
   #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'  
+  #if $designc.use:
+   --design=$designc.design
+   #if $designc.sets.__str__ != '':
+    --sets='$designc.sets'  
    #end if
   #end if
   #if int($iters.__str__) > 0:
    --iters=$iters
-  #end if
+	 #end if
   $jumble
   #if $calc.__str__ != "None" and len($calc.__str__) > 0:
     --calc='$calc'
   #end if
-  #if $subsample.use.__str__ == 'yes':
+  #if $subsample.use:
    #if $subsample.subsample.__str__ != '':
      --subsample=$subsample.subsample
    #else
@@ -54,7 +54,7 @@
     -->
    
   
-  
+  
     
     
     
     
     
-  
+	
 
  
  
@@ -90,7 +90,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/rarefaction.single.xml
--- a/mothur/tools/mothur/rarefaction.single.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/rarefaction.single.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Generate intra-sample rarefaction curves for OTUs
  
   mothur_wrapper.py 
@@ -69,7 +69,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
@@ -78,7 +78,7 @@
 
 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.
+provides bioinformatics for the microbial ecology community
 
 .. _Mothur: http://www.mothur.org/wiki/Main_Page
 
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/remove.groups.xml
--- a/mothur/tools/mothur/remove.groups.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/remove.groups.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Remove groups from groups,fasta,names,list,taxonomy
  
   mothur_wrapper.py 
@@ -7,8 +7,12 @@
   ## adds .pick before the last extension to the input file
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__]
   --cmd='remove.groups'
-  --outputdir='$logfile.extra_files_path'
-  --group=$group_in
+	--outputdir='$logfile.extra_files_path'
+  #if isinstance($group_in.datatype, $__app__.datatypes_registry.get_datatype_by_extension('group').__class__):
+		--group=$group_in
+	#else
+		--count=$group_in
+	#end if
   #if $groupnames.source == 'groups':
    #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0:
     --groups=$groupnames.groups
@@ -45,7 +49,7 @@
   --result=#echo ','.join($results)
  
  
-  
+  
   
    
     
@@ -94,7 +98,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/remove.lineage.xml
--- a/mothur/tools/mothur/remove.lineage.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/remove.lineage.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -5,10 +5,17 @@
   #import re, os.path
   #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
   ## adds .pick before the last extension to the input file
-  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__]
   --cmd='remove.lineage'
-  --outputdir='$logfile.extra_files_path'
-  --taxonomy=$taxonomy
+	--outputdir='$logfile.extra_files_path'
+	#if $file.filetype.__str__ == "usetaxonomy"
+		--taxonomy=$file.taxonomy
+		#set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__]
+	#else
+		--constaxonomy=$file.constaxonomy
+		--shared=$file.shared
+		--list=$file.list
+		#set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy.__str__)) + ":'" + $taxonomy_out.__str__]
+	#end if
   --taxon="'$re.sub('(\s|,)+',',',$re.sub('\(\d+\)','',$taxon.value.__str__))'"
   #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0:
    --fasta=$fasta_in
@@ -28,13 +35,29 @@
   #end if
   #if $name_in.__str__ != "None" and len($name_in.__str__) > 0:
    --name=$name_in
-   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__]
+	#set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__]
    $dups
   #end if
   --result=#echo ','.join($results)
+	#if $count.__str__ != "None" and len($count.__str__) > 0:
+		--count=$count
+	#end if
  
  
-  
+	 
+	 
+		 
+		 
+	 
+	 
+		
+	 
+	 
+		
+		
+		
+	 
+ 
   
+
+
+  
+   
+    
+    
+   
+   
+   
+    
+    
+      
+    
+    
+      
+    
+    
+      
+    
+    
+      
+    
+    
+      
+    
+   
+  
+
+
+
   
   
   
@@ -53,7 +107,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/shhh.flows.xml
--- a/mothur/tools/mothur/shhh.flows.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/shhh.flows.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Denoise flowgrams (PyroNoise algorithm)
  
   mothur_wrapper.py 
@@ -39,9 +39,7 @@
    
     
-     
-      
-      
+     
      
     
    
@@ -70,8 +68,8 @@
    
   
 
-  
+  
 
   
       
@@ -86,7 +84,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/shhh.seqs.xml
--- a/mothur/tools/mothur/shhh.seqs.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/shhh.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Denoise program (Quince SeqNoise)
  
   mothur_wrapper.py 
@@ -32,7 +32,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/sort.seqs.xml
--- a/mothur/tools/mothur/sort.seqs.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/sort.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  put sequences in different files in the same order
  
   mothur_wrapper.py 
@@ -36,6 +36,9 @@
   #end if
   $large
   --result=#echo ','.join($results)
+#if $count.__str__ != "None" and len($count.__str__) > 0:
+	--count=$count
+#end if
  
  
   
@@ -46,6 +49,7 @@
   
   
   
+
  
  
   
@@ -69,7 +73,7 @@
   
  
  
-  mothur
+mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/split.abund.xml
--- a/mothur/tools/mothur/split.abund.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/split.abund.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -29,6 +29,8 @@
    #if $accnos:
      #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.accnos)$',$os.path.basename($search.input.__str__)) + ":accnos'"]
    #end if
+	#else
+   --count=$search.input
   #end if
   --cutoff=$cutoff
   #if $split.type == 'yes':
@@ -52,6 +54,7 @@
    
     
     
+    
    
    
     
@@ -64,6 +67,9 @@
      
     
    
+	 
+    
+	 
    
   
   
@@ -98,7 +104,7 @@
   -->
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/split.groups.xml
--- a/mothur/tools/mothur/split.groups.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/split.groups.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Generates a fasta file for each group
  
   mothur_wrapper.py 
@@ -15,6 +15,9 @@
   #if $groups.__str__ != "None" and len($groups.__str__) > 0:
    --groups=$groups
   #end if
+	#if $count.__str__ != "None" and len($count.__str__) > 0:
+		--count=$count
+	#end if
  
  
   
@@ -25,12 +28,13 @@
     
    
   
+	
  
  
   
  
  
-  mothur
+mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/sub.sample.xml
--- a/mothur/tools/mothur/sub.sample.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/sub.sample.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Create a sub sample
  
   mothur_wrapper.py 
@@ -66,6 +66,12 @@
    --size=$size
   #end if
   --result=#echo ','.join($results)
+	#if $count.__str__ != "None" and len($count.__str__) > 0:
+		--count=$count
+	#end if
+	#if $taxonomy.__str__ != "None" and len($taxonomy.__str__) > 0:
+		--taxonomy=$taxtaxonomy
+	#end if
  
  
   
@@ -151,6 +157,8 @@
     
    
   
+	
+	
  
  
   
@@ -179,7 +187,7 @@
   
  
  
-  mothur
+mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/summary.qual.xml
--- a/mothur/tools/mothur/summary.qual.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/summary.qual.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Summarize the quality scores
  
   mothur_wrapper.py 
@@ -10,17 +10,21 @@
    --name=$name
   #end if
   ## --processors=8
+#if $count.__str__ != "None" and len($count.__str__) > 0:
+	--count=$count
+#end if
  
  
   
   
+
  
  
   
   
  
  
-  mothur
+mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/summary.seqs.xml
--- a/mothur/tools/mothur/summary.seqs.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/summary.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Summarize the quality of sequences
  
   mothur_wrapper.py 
@@ -9,18 +9,25 @@
   #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
+
  --processors=8
  
  
   
   
+  
  
  
   
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/summary.shared.xml
--- a/mothur/tools/mothur/summary.shared.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/summary.shared.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Summary of calculator values for OTUs
  
   mothur_wrapper.py 
@@ -121,7 +121,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/summary.single.xml
--- a/mothur/tools/mothur/summary.single.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/summary.single.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Summary of calculator values for OTUs
  
   mothur_wrapper.py 
@@ -107,7 +107,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/summary.tax.xml
--- a/mothur/tools/mothur/summary.tax.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/summary.tax.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Assign sequences to taxonomy
  
   mothur_wrapper.py 
@@ -15,6 +15,10 @@
   #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0:
    --reftaxonomy=$reftax.taxonomy
   #end if
+	#if $count.__str__ != "None" and len($count.__str__) > 0:
+		--count=$count
+	#end if
+	$relabund
  
  
   
@@ -24,9 +28,7 @@
    
    
     
-     
-      
-      
+     
      
     
    
@@ -45,9 +47,7 @@
    
    
     
-     
-      
-      
+     
      
     
    
@@ -55,13 +55,15 @@
     
    
   
+	
+
  
  
   
   
  
  
-  mothur
+mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/tree.shared.xml
--- a/mothur/tools/mothur/tree.shared.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/tree.shared.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Generate a newick tree for dissimilarity among groups
  
   mothur_wrapper.py 
@@ -37,6 +37,8 @@
     #if $input.name.__str__ != "None" and len($input.name.__str__) > 0:
      --name=$input.name
     #end if
+	 #else
+	 	--count=$input.name
    #end if
   #end if
   #if $calc.__str__ != "None" and len($calc.__str__) > 0:
@@ -51,6 +53,7 @@
     
     
     
+    
    
    
     
@@ -84,7 +87,11 @@
       
       
       
-   
+	 
+	 
+		
+    
+	 
   
   
    
@@ -136,7 +143,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/trim.flows.xml
--- a/mothur/tools/mothur/trim.flows.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/trim.flows.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  partition by barcode, trim to length, cull by lenght and mismatches
  
   mothur_wrapper.py 
@@ -97,8 +97,8 @@
          help="default .7">
    
   
-  
+  
 
   
 
@@ -115,7 +115,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/trim.seqs.xml
--- a/mothur/tools/mothur/trim.seqs.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/trim.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Trim sequences - primers, barcodes, quality
  
   mothur_wrapper.py 
@@ -74,6 +74,12 @@
   #if $names.__str__ != "None" and len($names.__str__) > 0:
    --name=$names
   #end if
+
+  $logtransform
+  $checkorient
+  #if $count.__str__ != "None" and len($count.__str__) > 0:
+    --count=$count
+  #end if
   --processors=8
  
  
@@ -132,6 +138,16 @@
    
   
   
+
+
+  
+  
+  
+
+
  
  
   
@@ -154,7 +170,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/unifrac.unweighted.xml
--- a/mothur/tools/mothur/unifrac.unweighted.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/unifrac.unweighted.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Describes whether two or more communities have the same structure
  
   mothur_wrapper.py 
@@ -41,6 +41,9 @@
   $root
   --result=#echo ','.join($results)
   --processors=1
+#if $count.__str__ != "None" and len($count.__str__) > 0:
+	--count=$count
+#end if
  
  
   
@@ -73,6 +76,7 @@
    
   
   
+
  
  
   
@@ -110,7 +114,7 @@
   
  
  
-  mothur
+mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/unifrac.weighted.xml
--- a/mothur/tools/mothur/unifrac.weighted.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/unifrac.weighted.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Describes whether two or more communities have the same structure
  
   mothur_wrapper.py 
@@ -41,6 +41,9 @@
   $root
   --result=#echo ','.join($results)
   --processors=8
+#if $count.__str__ != "None" and len($count.__str__) > 0:
+	--count=$count
+#end if
  
  
   
@@ -73,6 +76,7 @@
    
   
   
+
  
  
   
@@ -117,7 +121,7 @@
   
  
  
-  mothur
+mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/unique.seqs.xml
--- a/mothur/tools/mothur/unique.seqs.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/unique.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Return unique sequences
  
   mothur_wrapper.py 
@@ -9,10 +9,17 @@
   #if $names.__str__ != "None" and len($names.__str__) > 0:
    --name=$names
   #end if
+
+  #if $count.__str__ != "None" and len($count.__str__) > 0:
+    --count=$count
+  #end if
  
  
   
   
+
+  
  
  
   
@@ -20,7 +27,7 @@
   
  
  
-  mothur
+  mothur
  
  
  
diff -r 1be61ceb20d7 -r 95d75b35e4d2 mothur/tools/mothur/venn.xml
--- a/mothur/tools/mothur/venn.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/venn.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-
+
  Generate Venn diagrams for groups 
  
   mothur_wrapper.py 
@@ -37,6 +37,7 @@
   #if 100 > $fontsize > 0:
    --fontsize=$fontsize
   #end if
+	$sharedotus
  
  
   
@@ -83,12 +84,13 @@
   
   
   
+		
  
  
   
  
  
-  mothur
+  mothur