Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/amova.xml @ 25:bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 16 May 2012 12:28:44 -0500 |
parents | e990ac8a0f58 |
children | 49058b1f8d3f |
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<tool id="mothur_amova" name="Amova" version="1.19.0"> <description>Analysis of molecular variance</description> <command interpreter="python"> mothur_wrapper.py --cmd='amova' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.amova$:'$amova --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=$alpha #end if </command> <inputs> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 TAB-separated columns: group and grouping (Tool: Make_Design) "/> <param name="alpha" type="float" optional="true" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/> <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="amova" label="${tool.name} on ${on_string}: amova"/> </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 amova_ command calculates the analysis of molecular variance from a phylip_distance_matrix_, a nonparametric analog of traditional analysis of variance. This method is widely used in population genetics to test the hypothesis that genetic diversity within two populations is not significantly different from that which would result from pooling the two populations. 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 .. _amova: http://www.mothur.org/wiki/Amova </help> </tool>