Mercurial > repos > iuc > mothur_homova

annotate homova.xml @ 4:9a215084d776 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author iuc
date Mon, 23 Apr 2018 09:30:06 -0400
parents 2ccbfa78b831
children 68005ede9e6e
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1 <tool profile="16.07" id="mothur_homova" name="Homova" version="@WRAPPER_VERSION@.0">
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2 <description>Homogeneity of molecular variance</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$dist' dist.dat &&
2ccbfa78b831 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$design' design.dat &&
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15
2
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16 echo 'homova(
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17 phylip=dist.dat,
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18 design=design.dat,
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19 #if $sets:
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20 sets=${ str($sets).replace(",","-") },
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21 #end if
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22 iters=$iters,
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23 alpha=$alpha
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24 )'
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25 | sed 's/ //g' ## mothur trips over whitespace
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26 | mothur
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27 | tee mothur.out.log
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28 ]]></command>
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29 <inputs>
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30 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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31 <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
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32 <param name="alpha" type="float" optional="true" value="0.05" min="0.0" label="alpha - acceptable stopping precision (default 0.05)"/>
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33 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/>
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34 <param name="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze. The set names are separated by dashes. The default is all sets in designfile">
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35 <options>
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36 <filter type="data_meta" ref="design" key="groups"/>
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37 </options>
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38 </param>
2
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39 <expand macro="param-savelog"/>
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40 </inputs>
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41 <outputs>
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42 <expand macro="logfile-output"/>
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43 <data name="homova" format="tabular" from_work_dir="dist*.homova" label="${tool.name} on ${on_string}: homova"/>
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44 </outputs>
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45 <tests>
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46 <test><!-- test default settings -->
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47 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
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48 <param name="design" value="amazon.design" ftype="tabular"/>
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49 <output name="homova" ftype="tabular">
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50 <assert_contents>
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51 <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/>
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52 <has_text text="A-B"/>
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53 </assert_contents>
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54 </output>
2
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55 <param name="savelog" value="true"/>
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56 <expand macro="logfile-test"/>
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57 </test>
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58 <test><!-- test with subsets -->
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59 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
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60 <param name="design" value="amazon.design" ftype="mothur.design"/>
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61 <param name="sets" value="A"/>
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62 <output name="homova" ftype="tabular">
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63 <assert_contents>
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64 <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/>
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65 <has_line_matching expression="A\t.*$"/>
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66 </assert_contents>
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67 </output>
2
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68 <param name="savelog" value="true"/>
0
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69 <expand macro="logfile-test"/>
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70 </test>
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71 </tests>
2
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72 <help><![CDATA[
0
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73
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74 @MOTHUR_OVERVIEW@
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75
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76 **Command Documentation**
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77
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78 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.
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79
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80 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. :
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81 ======= =======
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82 duck bird
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83 cow mammal
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84 pig mammal
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85 goose bird
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86 cobra reptile
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87 ======= =======
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88
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89 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
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90
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91 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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92 .. _homova: https://www.mothur.org/wiki/Homova
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93
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94 v.1.20.0: Updated to Mothur 1.33, added sets parameter
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95
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96 ]]></help>
0
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97 <expand macro="citations"/>
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98 </tool>