Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/pcoa.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
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date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
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<tool id="mothur_pcoa" name="Pcoa" version="1.20.0" > <description>Principal Coordinate Analysis for a distance matrix</description> <command interpreter="python"> mothur_wrapper.py --cmd='pcoa' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pcoa\.axes$:'$pcoa,'^\S+\.pcoa.loadings$:'$loadings --outputdir='$logfile.extra_files_path' --phylip=$phylip $metric </command> <inputs> <param name="phylip" type="data" format="lower.dist,square.dist" label="phylip - Phylip Distance Matrix"/> <param name="metric" type="boolean" truevalue="" falsevalue="--metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" /> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="axes" name="pcoa" label="${tool.name} on ${on_string}: pcoa.axes" /> <data format="tabular" name="loadings" label="${tool.name} on ${on_string}: loadings" /> </outputs> <requirements> <requirement type="package" version="1.33">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 pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_. .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _pcoa: http://www.mothur.org/wiki/Pcoa </help> </tool>