Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/libshuff.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_libshuff" name="Libshuff" version="1.19.0"> <description>Cramer-von Mises tests communities for the same structure</description> <command interpreter="python"> mothur_wrapper.py --cmd='libshuff' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.libshuff\.summary$:'$summary,'^\S+\.libshuff\.coverage$:'$coverage --outputdir='$logfile.extra_files_path' --phylip=$dist --group=$group #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if #if len($iters.__str__) > 0: --iters=$iters #end if $sim #if $form == "discrete": #if 1.0 >= float($form.step.__str__) > 0.0: --step=$form.step #end if #if 1.0 >= float($cutoff.__str__) > 0.0: --cutoff=$form.cutoff #end if #end if </command> <inputs> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="group" type="data" format="groups" label="group - Groups"/> <param name="groups" type="select" label="groups - Groups to condider" multiple="true"> <options> <filter type="data_meta" ref="group" key="groups" /> </options> </param> <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/> <param name="sim" type="boolean" checked="false" truevalue="--sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" help=""/> <conditional name="form"> <param name="form" type="select" label="form - Select a Clustering Method" help=""> <option value="integral" selected="true">Integral</option> <option value="discrete">Discrete</option> </param> <when value="integral"/> <when value="discrete"> <param name="step" type="float" value="0.0" label="step - Step size - ignored if not > 0" help="default value 0.10, smaller steps approach integral"/> <param name="cutoff" type="float" value="0.0" label="cutoff - Cutoff threshold - ignored if not > 0" help=""/> </when> </conditional> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary"/> <data format="tabular" name="coverage" label="${tool.name} on ${on_string}: coverage"/> </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 libshuff_ method is a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic. The significance of the test statistic indicates the probability that the communities have the same structure by chance. Because each pairwise comparison requires two significance tests, a correction for multiple comparisons (e.g. Bonferroni's correction) must be applied. .. _libshuff: http://www.mothur.org/wiki/Libshuff </help> </tool>