Mercurial > repos > iuc > mothur_amova

annotate amova.xml @ 11:353fe428054e draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 21:48:56 +0000
parents 5bcc2ec88c52
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6da360fb8d1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_amova" name="Amova" version="@WRAPPER_VERSION@.0">
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2 <description>Analysis 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>
6da360fb8d1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
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13 ln -s '$phylip' phylip.dat &&
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14 ln -s '$design' design.dat &&
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15
3
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16 echo 'amova(
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17 phylip=phylip.dat,
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18 iters=$iters,
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19 alpha=$alpha,
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20 #if $sets:
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21 sets=${ str($sets).replace(",","-") },
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22 #end if
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23 design=design.dat
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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>
3
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30 <param argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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31 <param argument="design" type="data" format="mothur.design" label="design - assign groups to new grouping"
cf9391d88c6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 help="design has 2 TAB-separated columns: group and grouping (Tool: Make_Design)"/>
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33 <param argument="alpha" type="float" optional="true" min="0" value="0.05" label="alpha - acceptable stopping precision" help="default: 0.05"/>
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34 <param argument="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try" help="default: 1000"/>
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35 <param name="sets" type="text" label="sets - Which of the sets in your design file you would like to analyze?" help="separate sets by dashes or commas, e.g. set1,set2 or set1-set2-set3"/>
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36 <!-- TODO: update galaxy datatypes to set metadata for design files, then can switch to a select box
cf9391d88c6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 <param argument="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze."
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38 help="The set names are separated by dashes. The defualt is all sets in designfile">
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39 <options>
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40 <filter type="data_meta" ref="design" key="sets"/>
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41 </options>
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42 </param>
3
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43 -->
4
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44 <expand macro="param-savelog"/>
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45 </inputs>
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46 <outputs>
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47 <expand macro="logfile-output"/>
3
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48 <data name="amova" format="tabular" from_work_dir="phylip.amova" label="${tool.name} on ${on_string}: amova"/>
0
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49 </outputs>
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50 <tests>
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51 <test>
3
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52 <param name="phylip" value="amazon.dist"/>
0
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53 <param name="design" value="amazon.design"/>
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54 <output name="amova" ftype="tabular">
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55 <assert_contents>
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56 <has_line_matching expression="^A-B\tAmong\tWithin\tTotal$"/>
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57 <has_line_matching expression="^SS\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/>
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58 <has_line_matching expression="^df\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/>
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59 <has_line_matching expression="^MS\t[0-9\.]+\t[0-9\.]+$"/>
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60 <has_text text="p-value"/>
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61 </assert_contents>
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62 </output>
4
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63 <param name="savelog" value="true"/>
0
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64 <expand macro="logfile-test"/>
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65 </test>
3
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66 <test><!-- test with sets specified -->
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67 <param name="phylip" value="amazon.dist"/>
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68 <param name="design" value="amazon.design"/>
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69 <param name="sets" value="A,B"/>
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70 <output name="amova" ftype="tabular">
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71 <assert_contents>
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72 <has_line_matching expression="^A-B\tAmong\tWithin\tTotal$"/>
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73 <has_line_matching expression="^SS\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/>
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74 <has_line_matching expression="^df\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/>
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75 <has_line_matching expression="^MS\t[0-9\.]+\t[0-9\.]+$"/>
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76 <has_text text="p-value"/>
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77 </assert_contents>
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78 </output>
4
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79 <param name="savelog" value="true"/>
3
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80 <expand macro="logfile-test"/>
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81 </test>
0
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82 </tests>
3
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83 <help><![CDATA[
0
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84
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85 @MOTHUR_OVERVIEW@
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86
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87 **Command Documentation**
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88
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89 The amova_ command calculates the analysis of molecular variance from a phylip_distance_matrix_,
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90 a nonparametric analog of traditional analysis of variance. This method is widely used in population
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91 genetics to test the hypothesis that genetic diversity within two populations is not significantly
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92 different from that which would result from pooling the two populations.
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93
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94 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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95 ======= =======
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96 duck bird
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97 cow mammal
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98 pig mammal
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99 goose bird
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100 cobra reptile
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101 ======= =======
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102
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103 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
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104
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105
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106 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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107 .. _amova: https://www.mothur.org/wiki/Amova
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108
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109 ]]></help>
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110 <expand macro="citations">
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111 <citation type="doi">10.1111/j.1442-9993.2001.01070.pp.x</citation>
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112 </expand>
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113 </tool>