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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance"
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3 version="2020.8">
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4 <description>Beta diversity group significance</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime diversity beta-group-significance
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10
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11 --i-distance-matrix=$idistancematrix
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12 # if $input_files_mmetadatafile:
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13 # def list_dict_to_string(list_dict):
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14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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15 # for d in list_dict[1:]:
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16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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17 # end for
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18 # return $file_list
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19 # end def
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20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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21 # end if
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22
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23 #if '__ob__' in str($mmetadatacolumn):
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24 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
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25 #set $mmetadatacolumn = $mmetadatacolumn_temp
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26 #end if
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27 #if '__cb__' in str($mmetadatacolumn):
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28 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
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29 #set $mmetadatacolumn = $mmetadatacolumn_temp
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30 #end if
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31 #if 'X' in str($mmetadatacolumn):
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32 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
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33 #set $mmetadatacolumn = $mmetadatacolumn_temp
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34 #end if
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35 #if '__sq__' in str($mmetadatacolumn):
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36 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
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37 #set $mmetadatacolumn = $mmetadatacolumn_temp
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38 #end if
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39 #if '__db__' in str($mmetadatacolumn):
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40 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
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41 #set $mmetadatacolumn = $mmetadatacolumn_temp
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42 #end if
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43
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44 --m-metadata-column=$mmetadatacolumn
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45
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46
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47 #if str($pmethod) != 'None':
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48 --p-method=$pmethod
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49 #end if
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50
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51 #if $ppairwise:
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52 --p-pairwise
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53 #end if
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54
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55 --p-permutations=$ppermutations
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56
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57 --o-visualization=ovisualization
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58
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59 #if str($examples) != 'None':
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60 --examples=$examples
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61 #end if
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62
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63 ;
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64 cp odistancematrix.qza $odistancematrix
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65
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66 ;
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67 qiime tools export omantelscattervisualization.qzv --output-path out
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68 && mkdir -p '$omantelscattervisualization.files_path'
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69 && cp -r out/* '$omantelscattervisualization.files_path'
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70 && mv '$omantelscattervisualization.files_path/index.html' '$omantelscattervisualization'
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71
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72 ;
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73 qiime tools export ovisualization.qzv --output-path out
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74 && mkdir -p '$ovisualization.files_path'
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75 && cp -r out/* '$ovisualization.files_path'
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76 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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77
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78 ]]></command>
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79 <inputs>
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80 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
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81 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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82 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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83 </repeat>
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84 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical sample metadata column. [required]" name="mmetadatacolumn" optional="False" type="text" />
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85 <param label="--p-method: " name="pmethod" optional="True" type="select">
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86 <option selected="True" value="None">Selection is Optional</option>
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87 <option value="permanova">permanova</option>
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88 <option value="anosim">anosim</option>
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89 <option value="permdisp">permdisp</option>
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90 </param>
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91 <param label="--p-pairwise: --p-pairwise: / --p-no-pairwise Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column. [default: False]" name="ppairwise" selected="False" type="boolean" />
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92 <param label="--p-permutations: INTEGER The number of permutations to be run when computing p-values. [default: 999]" name="ppermutations" optional="True" type="integer" value="999" />
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93 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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94
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95 </inputs>
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96
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97 <outputs>
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98 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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99
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100 </outputs>
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101
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102 <help><![CDATA[
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103 Beta diversity group significance
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104 ###############################################################
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105
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106 Determine whether groups of samples are significantly different from one
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107 another using a permutation-based statistical test.
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108
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109 Parameters
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110 ----------
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111 distance_matrix : DistanceMatrix
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112 Matrix of distances between pairs of samples.
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113 metadata : MetadataColumn[Categorical]
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114 Categorical sample metadata column.
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115 method : Str % Choices('permanova', 'anosim', 'permdisp'), optional
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116 The group significance test to be applied.
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117 pairwise : Bool, optional
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118 Perform pairwise tests between all pairs of groups in addition to the
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119 test across all groups. This can be very slow if there are a lot of
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120 groups in the metadata column.
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121 permutations : Int, optional
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122 The number of permutations to be run when computing p-values.
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123
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124 Returns
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125 -------
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126 visualization : Visualization
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127 ]]></help>
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128 <macros>
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129 <import>qiime_citation.xml</import>
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130 </macros>
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131 <expand macro="qiime_citation"/>
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132 </tool> |
