Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/clearcut.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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<tool id="mothur_clearcut" name="Clearcut" version="1.19.0"> <description>Generate a tree using relaxed neighbor joining</description> <command interpreter="python"> mothur_wrapper.py --cmd='clearcut' #if $matrixout == True or $matrixout.__str__ == "true": --matrixout='matrixout.dist' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tree,'^matrixout\.dist$:'$matrix #else --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tree #end if --outputdir='$logfile.extra_files_path' #if $input.source == 'dna': --fasta=$input.fasta --DNA=true #elif $input.source == 'aa': --fasta=$input.fasta --protein=true #elif $input.source == 'phylip': --phylip=$input.dist #end if #if int($seed.__str__) >= 0: --seed=$seed #end if #if int($ntrees.__str__) > 1: --ntrees=$ntrees #end if $norandom $shuffle $neighbor </command> <inputs> <!-- get.relabund relabund type should also work --> <conditional name="input"> <param name="source" type="select" label="Distance Matrix"> <option value="dna">DNA Alignment Fasta</option> <option value="aa">Protein Alignment Fasta</option> <option value="phylip">Phylip Distance Matrix</option> </param> <when value="dna"> <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/> </when> <when value="aa"> <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/> </when> <when value="phylip"> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> </when> </conditional> <param name="seed" type="integer" value="-1" label="seed - Set the PRNG seed to a specific value (ignored if negative)"/> <param name="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (ignored if < 1)"/> <param name="norandom" type="boolean" checked="false" truevalue="--norandom=true" falsevalue="" label="norandom - Attempt joins deterministically"/> <param name="shuffle" type="boolean" checked="false" truevalue="--shuffle=true" falsevalue="" label="shuffle - Randomly shuffle the distance matrix"/> <param name="neighbor" type="boolean" checked="false" truevalue="--neighbor=true" falsevalue="" label="neighbor - Use traditional Neighbor-Joining algorithm"/> <param name="expblen" type="boolean" checked="false" truevalue="--expblen=true" falsevalue="" label="expblen - Use exponential notation for branch lengths"/> <param name="expdist" type="boolean" checked="false" truevalue="--expdist=true" falsevalue="" label="expdist - Use exponential notation for distance"/> <param name="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="" label="matrixout - Generate a Distance Matrix"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tre" name="tree" label="${tool.name} on ${on_string}: tree" /> <data format="lower.dist" name="matrix" label="${tool.name} on ${on_string}: Phylip Distance Matrix" > <filter>matrixout == True</filter> </data> </outputs> <requirements> <requirement type="package" version="1.27">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 clearcut_ command runs clearcut The clearcut command allows mothur users to run the clearcut_program_ from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. For more information about clearcut please refer to http://bioinformatics.hungry.com/clearcut/ Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ). Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input. If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura). Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix. .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/ .. _clearcut: http://www.mothur.org/wiki/Clearcut </help> </tool>