Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/chimera.uchime.xml @ 15:a6189f58fedb
Mothur - updated for Mothur version 1.22.0
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 08 Nov 2011 11:45:32 -0600 |
parents | 4f797d3eee3a |
children | 49058b1f8d3f |
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<tool id="mothur_chimera_uchime" name="Chimera.uchime" version="1.22.0"> <description>Find putative chimeras using uchime</description> <command interpreter="python"> mothur_wrapper.py --cmd='chimera.uchime' ## stool.trim.unique.good.fasta ## stool.trim.unique.good.uchime.chimera ## stool.trim.unique.good.uchime.accnos ## stool.trim.unique.good.uchime.alns #if $chimealns: --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.uchime\.chimeras?$:'$out_file,'^\S+\.uchime\.accnos$:'$out_accnos,'^\S+\.uchime\.alns$:'$out_alns #else: --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.uchime\.chimeras?$:'$out_file,'^\S+\.uchime\.accnos$:'$out_accnos #end if --outputdir='$logfile.extra_files_path' --fasta=$fasta #if $template.source == 'ref': --reference=$template.reference #elif $template.source == 'hist': --reference=$template.reference #elif $template.source == 'self': --reference='self' #if float($template.abskew.__str__) > 0: --abskew=$template.abskew #end if #if $template.group.__str__ != '': --group=$template.group #end if #elif $template.source == 'names': --name=$template.name #end if #if float($minh.__str__) > 0: --minh=$minh #end if #if float($mindiv.__str__) > 0: --mindiv=$mindiv #end if #if float($xn.__str__) > 0: --xn=$xn #end if #if float($dn.__str__) > 0: --dn=$dn #end if #if float($xa.__str__) > 0: --xa=$xa #end if #if int($chunks.__str__) > 0: --chunks=$chunks #end if #if int($minchunk.__str__) > 0: --minchunk=$minchunk #end if #if len($idsmoothwindow.__str__) > 0 and int($idsmoothwindow.__str__) > 0: --idsmoothwindow=$idsmoothwindow #end if ## #if len($minsmoothid.__str__) > 0 and float($minsmoothid.__str__) > 0: ## --minsmoothid=$minsmoothid ## #end if #if int($maxp.__str__) > 0: --maxp=$maxp #end if #if int($minlen.__str__) > 0: --minlen=$minlen #end if #if int($maxlen.__str__) > 0: --maxlen=$maxlen #end if $skipgaps $skipgaps2 #if $alignment.ucl: --ucl=true #if $alignment.queryfract != None and len($alignment.queryfract) > 0 and 1.0 >= float($alignment.queryfract) > 0: --queryfract=$alignment.queryfract #end if #end if $chimealns --processors=8 </command> <inputs> <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/> <conditional name="template"> <param name="source" type="select" label="Select Reference Template from" help=""> <option value="hist">History</option> <option value="ref">Cached Reference</option> <option value="self">Self</option> <option value="names">Use a names file</option> </param> <when value="ref"> <param name="reference" type="select" label="reference - Select an alignment database " help=""> <options from_file="mothur_aligndb.loc"> <column name="name" index="0" /> <column name="value" index="1" /> </options> </param> </when> <when value="hist"> <param name="reference" type="data" format="fasta" label="reference - Reference to align with" help=""/> </when> <when value="self"> <param name="abskew" type="float" value="1.9" label="abskew - Abundance skew (default 1.9)" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query)"/> <param name="group" type="data" format="groups" optional="true" label="group - Sequences Name reference" help="use the more abundant sequences from the same sample to check the query sequence"/> </when> <when value="names"> <param name="name" type="data" format="names" label="name - Sequence names"/> </when> </conditional> <param name="minh" type="float" value="0.3" label="minh - mininum score to report chimera. Default 0.3" help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/> <param name="mindiv" type="float" value="0.5" label="mindiv - minimum divergence ratio, default 0.5" help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1"/> <param name="xn" type="float" value="8.0" label="xn - weight of a no vote. Default 8.0" help="Decreasing this weight to around 3 or 4 may give better performance on denoised data"/> <param name="dn" type="float" value="1.4" label="dn - pseudo-count prior on number of no votes. Default 1.4" help="Reasonable values are probably in the range from 0.2 to 2.0"/> <param name="xa" type="float" value="1.0" label="xa - eight of an abstain vote. Default 1.0" help="Reasonable values might range from 0.1 to 2.0"/> <param name="chunks" type="integer" value="4" label="chunks - number of chunks. Default 4." help="number of chunks to extract from the query sequence when searching for parents."/> <param name="minchunk" type="integer" value="64" label="minchunk - minimum length of a chunk. Default 64." help=""/> <param name="idsmoothwindow" type="integer" value="32" optional="True" label="idsmoothwindow - the length of id smoothing window. Default 32" help=""/> <!-- not supported in uchime <param name="minsmoothid" type="float" value="0.95" optional="True" label="minsmoothid - minimum factional identity over smoothed window of candidate parent. Default 0.95" help=""/> --> <param name="maxp" type="integer" value="2" label="maxp - maximum number of candidate parents to consider. Default 2" help="increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit"/> <param name="minlen" type="integer" value="0" label="minlen - minimum unaligned sequence length. Default 10" help="Applies to both query and reference sequences."/> <param name="maxlen" type="integer" value="0" label="maxlen - maximum unaligned sequence length. Defaults 10000" help="Applies to both query and reference sequences."/> <param name="skipgaps" type="boolean" falsevalue="--skipgaps=false" truevalue="" checked="true" label="skipgaps - columns containing gaps do not count as diffs. Default=T" help="controls how gapped columns affect counting of diffs"/> <param name="skipgaps2" type="boolean" falsevalue="--skipgaps2=false" truevalue="" checked="true" label="skipgaps2 - column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default=T" help="controls how gapped columns affect counting of diffs"/> <param name="chimealns" type="boolean" falsevalue="" truevalue="--chimealns=true" checked="false" label="chimealns - Produce a file containing multiple alignments of query sequences to parents in human readable format. " help="Alignments show columns with differences that support or contradict a chimeric model."/> <conditional name="alignment"> <param name="ucl" type="boolean" falsevalue="global" truevalue="local" checked="false" label="ucl - Use local-X alignments." help="global-X is the default"/> <when value="global"/> <when value="local"> <param name="queryfract" type="float" value="0.5" label="queryfract - minimum fraction of the query sequence that must be covered by a local-X alignment. Default 0.5." help=""/> </when> </conditional> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="txt" name="out_file" label="${tool.name} on ${on_string}: uchime.chimeras" /> <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: uchime.accnos" /> <data format="txt" name="out_alns" label="${tool.name} on ${on_string}: uchime.alns" > <filter>chimealns == True</filter> </data> </outputs> <requirements> <requirement type="binary">mothur</requirement> </requirements> <tests> </tests> <help> **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 chimera.uchime_ command reads a fasta file and reference file and outputs potentially chimeric sequences. The original uchime program was written by Robert C. Edgar and donated to the public domain, http://drive5.com/uchime .. _chimera.uchime: http://www.mothur.org/wiki/Chimera.uchime </help> </tool>