Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/nmds.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
parents | 95d75b35e4d2 |
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<tool id="mothur_nmds" name="Nmds" version="1.20.0"> <description>generate non-metric multidimensional scaling data</description> <command interpreter="python"> mothur_wrapper.py --cmd='nmds' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.nmds\.axes$:'$nmds_axes,'^\S+\.nmds\.iters$:'$nmds_iters,'^\S+\.nmds\.stress$:'$stress_nmds --outputdir='$logfile.extra_files_path' --phylip=$dist #if $axes.__str__ != "None" and len($axes.__str__) > 0: --axes=$axes #end if #if int($mindim.__str__) > 0: --mindim=$mindim #end if #if int($maxdim.__str__) >= int($mindim.__str__): --maxdim=$maxdim #end if #if int($iters.__str__) > 0: --iters=$iters #end if #if int($maxiters.__str__) > 0: --maxiters=$maxiters #end if #if float($epsilon.__str__) > 0.0: --epsilon=$epsilon #end if </command> <inputs> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="axes" type="data" format="axes" optional="true" label="axes - a starting configuration"/> <param name="mindim" type="integer" value="2" label="mindim - minimum dimensions (default 2)"/> <param name="maxdim" type="integer" value="2" label="maxdim - maximum dimensions (default 2)"/> <param name="iters" type="integer" value="10" label="iters - Number of random configuration to try (default 10)"/> <param name="maxiters" type="integer" value="500" label="maxiters - Number of iterations to try with each random configuration (default 500)"/> <param name="epsilon" type="float" optional="true" value="1e-12" label="epsilon - acceptable stopping precision (default 1e-12)"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="axes" name="nmds_axes" label="${tool.name} on ${on_string}: nmds.axes"/> <data format="tabular" name="nmds_iters" label="${tool.name} on ${on_string}: nmds.iters"/> <data format="tabular" name="stress_nmds" label="${tool.name} on ${on_string}: nmds.stress"/> </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 nmds_ command generates non-metric multidimensional scaling data from a phylip_distance_matrix_. .. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _nmds: http://www.mothur.org/wiki/Nmds v1.20.0: Updated to mothur 1.33 </help> </tool>