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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity mantel --i-dm2=$idm2 --i-dm1=$idm1
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9
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10 #if $pintersectids:
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11 --p-intersect-ids
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12 #else
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13 --p-no-intersect-ids
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14 #end if
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15
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16 #if str($cmdconfig) != 'None':
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17 --cmd-config=$cmdconfig
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18 #end if
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19
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20 #if str($plabel2):
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21 --p-label2="$plabel2"
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22 #end if
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23
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24 #if str($plabel1):
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25 --p-label1="$plabel1"
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26 #end if
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27
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28 --o-visualization=ovisualization
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29
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30 #if str($pmethod) != 'None':
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31 --p-method=$pmethod
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32 #end if
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33
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34 #if $ppermutations:
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35 --p-permutations=$ppermutations
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36 #end if
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37 ;
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38 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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39 && cp -r out/* '$ovisualization.files_path'
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40 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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41 ]]></command>
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42 <inputs>
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43 <param format="qza,no_unzip.zip" label="--i-dm1: DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idm1" optional="False" type="data"/>
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44 <param format="qza,no_unzip.zip" label="--i-dm2: DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idm2" optional="False" type="data"/>
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45 <param label="--p-method: " name="pmethod" optional="True" type="select">
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46 <option selected="True" value="spearman">spearman</option>
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47 <option value="pearson">pearson</option>
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48 </param>
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49 <param label="--p-permutations: 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" value="999"/>
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50 <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" checked="False" type="boolean"/>
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51 <param label="--p-label1: 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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52 <param label="--p-label2: 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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53 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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54 </inputs>
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55 <outputs>
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56 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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57 </outputs>
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58 <help><![CDATA[
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59 Apply the Mantel test to two distance matrices
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60 ----------------------------------------------
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61
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62 Apply a two-sided Mantel test to identify correlation between two distance
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63 matrices. Note: the directionality of the comparison has no bearing on the
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64 results. Thus, comparing distance matrix X to distance matrix Y is
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65 equivalent to comparing Y to X. Note: the order of samples within the two
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66 distance matrices does not need to be the same; the distance matrices will
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67 be reordered before applying the Mantel test. See the scikit-bio docs for
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68 more details about the Mantel test: http://scikit-
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69 bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html
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70
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71 Parameters
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72 ----------
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73 dm1 : DistanceMatrix
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74 Matrix of distances between pairs of samples.
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75 dm2 : DistanceMatrix
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76 Matrix of distances between pairs of samples.
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77 method : Str % Choices({'pearson', 'spearman'}), optional
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78 The correlation test to be applied in the Mantel test.
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79 permutations : Int % Range(0, None), optional
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80 The number of permutations to be run when computing p-values. Supplying
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81 a value of zero will disable permutation testing and p-values will not
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82 be calculated (this results in *much* quicker execution time if
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83 p-values are not desired).
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84 intersect_ids : Bool, optional
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85 If supplied, IDs that are not found in both distance matrices will be
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86 discarded before applying the Mantel test. Default behavior is to error
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87 on any mismatched IDs.
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88 label1 : Str, optional
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89 Label for \`dm1\` in the output visualization.
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90 label2 : Str, optional
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91 Label for \`dm2\` in the output visualization.
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92
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93 Returns
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94 -------
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95 visualization : Visualization
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96 \
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97 ]]>
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98 </help>
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99 <macros>
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100 <import>qiime_citation.xml</import>
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101 </macros>
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102 <expand macro="qiime_citation" />
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103 </tool>
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