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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2019.7">
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3 <description> - Apply the Mantel test to two distance matrices</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity mantel
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9
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10 --i-dm1=$idm1
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11 --i-dm2=$idm2
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12
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13 #if str($pmethod) != 'None':
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14 --p-method=$pmethod
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15 #end if
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16
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17 #if str($ppermutations):
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18 --p-permutations=$ppermutations
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19 #end if
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20
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21 #if $pintersectids:
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22 --p-intersect-ids
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23 #end if
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24
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25
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26
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27 #if '__sq__' in str($plabel1):
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28 #set $plabel1_temp = $plabel1.replace('__sq__', "'")
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29 #set $plabel1 = $plabel1_temp
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30 #end if
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31
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32 #if str($plabel1):
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33 --p-label1="$plabel1"
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34 #end if
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35
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36
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37
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38 #if '__sq__' in str($plabel2):
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39 #set $plabel2_temp = $plabel2.replace('__sq__', "'")
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40 #set $plabel2 = $plabel2_temp
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41 #end if
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42
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43 #if str($plabel2):
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44 --p-label2="$plabel2"
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45 #end if
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46
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47
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48
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49 --o-visualization=ovisualization
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50 ;
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51 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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52 && cp -r out/* '$ovisualization.files_path'
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53 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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54 ]]></command>
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55 <inputs>
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56 <param format="qza,no_unzip.zip" label="--i-dm1: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm1" optional="False" type="data"/>
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57 <param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm2" optional="False" type="data"/>
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58 <param label="--p-method: " name="pmethod" optional="True" type="select">
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59 <option selected="True" value="None">Selection is Optional</option>
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60 <option value="spearman">spearman</option>
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61 <option value="pearson">pearson</option>
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62 </param>
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63 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
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64 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/>
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65 <param label="--p-label1: TEXT Label for `dm1` in the output visualization. [default: 'Distance Matrix 1']" name="plabel1" optional="True" type="text" value="Distance Matrix 1"/>
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66 <param label="--p-label2: TEXT Label for `dm2` in the output visualization. [default: 'Distance Matrix 2']" name="plabel2" optional="True" type="text" value="Distance Matrix 2"/>
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67 </inputs>
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68 <outputs>
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69 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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70 </outputs>
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71 <help><![CDATA[
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72 Apply the Mantel test to two distance matrices
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73 ##############################################
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74
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75 Apply a two-sided Mantel test to identify correlation between two distance
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76 matrices. Note: the directionality of the comparison has no bearing on the
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77 results. Thus, comparing distance matrix X to distance matrix Y is
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78 equivalent to comparing Y to X. Note: the order of samples within the two
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79 distance matrices does not need to be the same; the distance matrices will
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80 be reordered before applying the Mantel test. See the scikit-bio docs for
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81 more details about the Mantel test: http://scikit-
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82 bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html
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83
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84 Parameters
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85 ----------
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86 dm1 : DistanceMatrix
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87 Matrix of distances between pairs of samples.
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88 dm2 : DistanceMatrix
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89 Matrix of distances between pairs of samples.
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90 method : Str % Choices('spearman', 'pearson'), optional
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91 The correlation test to be applied in the Mantel test.
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92 permutations : Int % Range(0, None), optional
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93 The number of permutations to be run when computing p-values. Supplying
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94 a value of zero will disable permutation testing and p-values will not
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95 be calculated (this results in *much* quicker execution time if
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96 p-values are not desired).
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97 intersect_ids : Bool, optional
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98 If supplied, IDs that are not found in both distance matrices will be
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99 discarded before applying the Mantel test. Default behavior is to error
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100 on any mismatched IDs.
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101 label1 : Str, optional
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102 Label for `dm1` in the output visualization.
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103 label2 : Str, optional
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104 Label for `dm2` in the output visualization.
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105
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106 Returns
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107 -------
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108 visualization : Visualization
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109 ]]></help>
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110 <macros>
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111 <import>qiime_citation.xml</import>
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112 </macros>
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113 <expand macro="qiime_citation"/>
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114 </tool>
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