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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity-lib_beta-phylogenetic-passthrough" name="qiime diversity-lib beta-phylogenetic-passthrough"
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3 version="2020.8">
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4 <description>Beta Phylogenetic Passthrough</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-lib beta-phylogenetic-passthrough
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10
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11 --i-table=$itable
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12
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13 --i-phylogeny=$iphylogeny
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14
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15 --p-metric=$pmetric
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16
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17 #if str($pthreads) != 'None':
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18 --p-threads=$pthreads
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19 #end if
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20
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21 #if $pvarianceadjusted:
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22 --p-variance-adjusted
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23 #end if
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24
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25 #if str($palpha):
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26 --p-alpha=$palpha
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27 #end if
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28 #if $pbypasstips:
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29 --p-bypass-tips
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30 #end if
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31
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32 --o-distance-matrix=odistancematrix
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33
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34 #if str($examples) != 'None':
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35 --examples=$examples
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36 #end if
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37
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38 ;
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39 cp odistancematrix.qza $odistancematrix
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40
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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-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed. [required]" name="itable" optional="False" type="data" />
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44 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data" />
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45 <param label="--p-metric: " name="pmetric" optional="False" type="select">
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46 <option value="weighted_unifrac">weighted_unifrac</option>
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47 <option value="unweighted_unifrac">unweighted_unifrac</option>
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48 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
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49 <option value="generalized_unifrac">generalized_unifrac</option>
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50 </param>
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51 <param label="--p-threads: " name="pthreads" optional="True" type="select">
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52 <option selected="True" value="None">Selection is Optional</option>
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53 <option value="Int % Range(1">Int % Range(1</option>
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54 <option value="None">None</option>
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55 </param>
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56 <param label="--p-variance-adjusted: --p-variance-adjusted: / --p-no-variance-adjusted Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]" name="pvarianceadjusted" selected="False" type="boolean" />
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57 <param label="--p-alpha: PROPORTION Range(0, 1, inclusive_end=True) This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized. [optional]" name="palpha" optional="False" type="text" />
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58 <param label="--p-bypass-tips: --p-bypass-tips: / --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]" name="pbypasstips" selected="False" type="boolean" />
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59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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60
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61 </inputs>
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62
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63 <outputs>
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64 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
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65
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66 </outputs>
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67
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68 <help><![CDATA[
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69 Beta Phylogenetic Passthrough
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70 ###############################################################
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71
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72 Computes a distance matrix for all pairs of samples in a feature table
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73 using the unifrac implementation of the selected beta diversity metric.
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74
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75 Parameters
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76 ----------
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77 table : FeatureTable[Frequency]
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78 The feature table containing the samples over which beta diversity
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79 should be computed.
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80 phylogeny : Phylogeny[Rooted]
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81 Phylogenetic tree containing tip identifiers that correspond to the
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82 feature identifiers in the table. This tree can contain tip ids that
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83 are not present in the table, but all feature ids in the table must be
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84 present in this tree.
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85 metric : Str % Choices('unweighted_unifrac', 'generalized_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac')
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86 The beta diversity metric to be computed.
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87 threads : Int % Range(1, None) | Str % Choices('auto'), optional
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88 The number of CPU threads to use in performing this calculation. May
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89 not exceed the number of available physical cores. If threads = 'auto',
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90 one thread will be created for each identified CPU core on the host.
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91 variance_adjusted : Bool, optional
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92 Perform variance adjustment based on Chang et al. BMC Bioinformatics
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93 2011. Weights distances based on the proportion of the relative
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94 abundance represented between the samples at a given node under
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95 evaluation.
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96 alpha : Float % Range(0, 1, inclusive_end=True), optional
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97 This parameter is only used when the choice of metric is
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98 generalized_unifrac. The value of alpha controls importance of sample
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99 proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to
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100 unweighted UniFrac, but only if the sample proportions are
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101 dichotomized.
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102 bypass_tips : Bool, optional
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103 In a bifurcating tree, the tips make up about 50% of the nodes in a
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104 tree. By ignoring them, specificity can be traded for reduced compute
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105 time. This has the effect of collapsing the phylogeny, and is analogous
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106 (in concept) to moving from 99% to 97% OTUs
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107
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108 Returns
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109 -------
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110 distance_matrix : DistanceMatrix
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111 The resulting distance matrix.
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112 ]]></help>
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113 <macros>
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114 <import>qiime_citation.xml</import>
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115 </macros>
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116 <expand macro="qiime_citation"/>
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117 </tool> |
