Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/homova.xml @ 13:4f797d3eee3a
Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 05 Oct 2011 10:34:44 -0500 |
parents | e990ac8a0f58 |
children | 49058b1f8d3f |
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<tool id="mothur_homova" name="Homova" version="1.19.0"> <description>Homogeneity of molecular variance</description> <command interpreter="python"> mothur_wrapper.py --cmd='homova' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.homova$:'$homova --outputdir='$logfile.extra_files_path' --phylip=$dist --design=$design #if int($iters.__str__) > 0: --iters=$iters #end if #if float($alpha.__str__) > 0.0: --alpha=$alpha #end if </command> <inputs> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> <param name="alpha" type="float" optional="true" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/> <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="homova" label="${tool.name} on ${on_string}: homova"/> </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 homova_ command calculates the homogeneity of molecular variance (HOMOVA) from a phylip_distance_matrix_, a nonparametric analog of Bartlett's test for homo- geneity of variance, which has been used in population genetics to test the hypothesis that the genetic diversity within two or more populations is homogeneous. A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. : ======= ======= duck bird cow mammal pig mammal goose bird cobra reptile ======= ======= The Make_Design tool can construct a design file from a Mothur dataset that contains group names. .. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _homova: http://www.mothur.org/wiki/Homova </help> </tool>