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annotate tools/mothur/homova.xml @ 0:ee4fee239fe7 draft default tip

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author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 echo 'homova(
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10 phylip=$dist,
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11 design=$design,
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12 #if $sets:
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13 sets=${ str($sets).replace(",","-") },
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14 #end if
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15 iters=$iters,
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16 alpha=$alpha
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17 )'
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18 | sed 's/ //g' ## mothur trips over whitespace
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19 | mothur &&
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20
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21 ## move output files to correct destination
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22 prefix="$dist" &&
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23 mv mothur.*.logfile "$logfile" &&
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24 mv \${prefix%.dat}*.homova "$homova"
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25 ]]></command>
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26 <inputs>
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27 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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28 <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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29 <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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30 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/>
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31 <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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32 <options>
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33 <filter type="data_meta" ref="design" key="groups"/>
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34 </options>
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35 </param>
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36 </inputs>
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37 <outputs>
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38 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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39 <data name="homova" format="tabular" label="${tool.name} on ${on_string}: homova"/>
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40 </outputs>
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41 <tests>
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42 <test><!-- test default settings -->
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43 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
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44 <param name="design" value="amazon.design" ftype="tabular"/>
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45 <output name="homova" ftype="tabular">
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46 <assert_contents>
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47 <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/>
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48 <has_text text="A-B"/>
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49 </assert_contents>
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50 </output>
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51 <expand macro="logfile-test"/>
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52 </test>
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53 <test><!-- test with subsets -->
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54 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
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55 <param name="design" value="amazon.design" ftype="mothur.design"/>
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56 <param name="sets" value="A"/>
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57 <output name="homova" ftype="tabular">
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58 <assert_contents>
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59 <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/>
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60 <has_line_matching expression="A\t.*$"/>
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61 </assert_contents>
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62 </output>
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63 <expand macro="logfile-test"/>
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64 </test>
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65 </tests>
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66 <help>
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67 <![CDATA[
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68
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69 @MOTHUR_OVERVIEW@
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70
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71 **Command Documenation**
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72
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73 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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74
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75 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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76 ======= =======
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77 duck bird
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78 cow mammal
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79 pig mammal
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80 goose bird
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81 cobra reptile
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82 ======= =======
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83
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84 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
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85
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86 .. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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87 .. _homova: http://www.mothur.org/wiki/Homova
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88
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89 v.1.20.0: Updated to Mothur 1.33, added sets parameter
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90 ]]>
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91 </help>
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92 <expand macro="citations"/>
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93 </tool>