Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/libshuff.xml @ 11:11867a45a43d
Change make.shared param name from unique to groups
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 14 Jul 2011 15:21:01 -0500 |
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1 <tool id="mothur_libshuff" name="Libshuff" version="1.19.0"> |
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2 <description>Cramer-von Mises tests communities for the same structure</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='libshuff' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.libshuff\.summary$:'$summary,'^\S+\.libshuff\.coverage$:'$coverage |
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7 --outputdir='$logfile.extra_files_path' |
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8 --phylip=$dist |
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9 --group=$group |
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10 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
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11 --groups=$groups |
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12 #end if |
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13 #if len($iters.__str__) > 0: |
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14 --iters=$iters |
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15 #end if |
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16 $sim |
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17 #if $form == "discrete": |
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18 #if 1.0 >= float($form.step.__str__) > 0.0: |
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19 --step=$form.step |
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20 #end if |
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21 #if 1.0 >= float($cutoff.__str__) > 0.0: |
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22 --cutoff=$form.cutoff |
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23 #end if |
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24 #end if |
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25 </command> |
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26 <inputs> |
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27 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
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28 <param name="group" type="data" format="groups" label="group - Groups"/> |
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29 <param name="groups" type="select" label="groups - Groups to condider" multiple="true"> |
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30 <options from_dataset="group"> |
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31 <column name="name" index="1"/> |
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32 <column name="value" index="1"/> |
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33 <filter type="unique_value" name="unq_grp" column="1" /> |
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34 </options> |
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35 </param> |
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36 <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/> |
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37 <param name="sim" type="boolean" checked="false" truevalue="--sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" help=""/> |
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38 <conditional name="form"> |
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39 <param name="form" type="select" label="form - Select a Clustering Method" help=""> |
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40 <option value="integral" selected="true">Integral</option> |
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41 <option value="discrete">Discrete</option> |
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42 </param> |
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43 <when value="integral"/> |
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44 <when value="discrete"> |
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45 <param name="step" type="float" value="0.0" label="step - Step size - ignored if not > 0" |
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46 help="default value 0.10, smaller steps approach integral"/> |
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47 <param name="cutoff" type="float" value="0.0" label="cutoff - Cutoff threshold - ignored if not > 0" help=""/> |
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48 </when> |
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49 </conditional> |
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50 </inputs> |
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51 <outputs> |
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52 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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53 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary"/> |
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54 <data format="tabular" name="coverage" label="${tool.name} on ${on_string}: coverage"/> |
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55 </outputs> |
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56 <requirements> |
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57 <requirement type="binary">mothur</requirement> |
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58 </requirements> |
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59 <tests> |
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60 </tests> |
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61 <help> |
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62 **Mothur Overview** |
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63 |
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64 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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65 in the Department of Microbiology and Immunology at The University of Michigan, |
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66 provides bioinformatics for the microbial ecology community. |
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67 |
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68 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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69 |
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70 **Command Documenation** |
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71 |
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72 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. |
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73 |
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74 .. _libshuff: http://www.mothur.org/wiki/Libshuff |
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75 |
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76 |
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77 </help> |
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78 </tool> |