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1 <?xml version="1.0" ?>
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2 <tool id="qiime_gneiss_balance-taxonomy" name="qiime gneiss balance-taxonomy" version="2019.7">
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3 <description> - Balance Summary</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 gneiss balance-taxonomy
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10
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11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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13 --i-taxonomy '$tax'
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14 #else:
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15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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16 --i-taxonomy '$tax'
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17 #end if
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18
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19
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20 --i-table=$itable
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21 --i-tree=$itree
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22 --p-balance-name="$pbalancename"
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23
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24
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25
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26 #if $metadatafile:
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27 --m-metadata-file=$metadatafile
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28 #end if
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29
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30
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31
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32 #if str($ppseudocount):
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33 --p-pseudocount=$ppseudocount
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34 #end if
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35
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36 #if str($ptaxalevel):
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37 --p-taxa-level=$ptaxalevel
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38 #end if
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39
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40 #if str($pnfeatures):
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41 --p-n-features=$pnfeatures
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42 #end if
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43
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44 #if str($pthreshold):
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45 --p-threshold="$pthreshold"
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46 #end if
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47 #if str($mmetadatacolumn):
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48 --m-metadata-column="$mmetadatacolumn"
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49 #end if
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50
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51 --o-visualization=ovisualization
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52 ;
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53 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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54 && cp -r out/* '$ovisualization.files_path'
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55 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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56 ]]></command>
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57 <inputs>
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58
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59 <conditional name="id_to_taxonomy_fp" optional="True">
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60 <param name="selector" type="select" label="Reference taxonomy to query">
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61 <option value="cached">Public databases</option>
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62 <option value="history">Databases from your history</option>
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63 </param>
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64 <when value="cached">
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65 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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66 <options from_data_table="qiime_taxonomy" />
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67 </param>
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68 </when>
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69 <when value="history">
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70 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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71 </when>
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72 </conditional>
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73
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74 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] A table of abundances. [required]" name="itable" optional="False" type="data"/>
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75 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree used to calculate the balances. Hierarchy [required]" name="itree" optional="False" type="data"/>
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76 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomy information for the OTUs. [required]" name="itaxonomy" optional="False" type="data"/>
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77 <param label="--p-balance-name: TEXT Name of the balance to summarize. [required]" name="pbalancename" optional="False" type="text"/>
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78 <param label="--p-pseudocount: NUMBER The pseudocount to add to avoid division by zero. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5"/>
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79 <param label="--p-taxa-level: INTEGER Level of taxonomy to summarize. [default: 0]" name="ptaxalevel" optional="True" type="integer" value="0"/>
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80 <param label="--p-n-features: INTEGER The number of features to plot in the proportion plot. [default: 10]" name="pnfeatures" optional="True" type="integer" value="10"/>
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81 <param label="--p-threshold: NUMBER A threshold to designate discrete categories for a numerical metadata column. This will split the numerical column values into two categories, values below the threshold, and values above the threshold. If not specified, this threshold will default to the mean. [optional]" name="pthreshold" optional="True" type="float"/>
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82 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical | Numeric] Metadata column for plotting the balance (optional). [optional]" name="mmetadatacolumn" optional="True" type="text"/>
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83
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84 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" optional="True" />
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85
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86 </inputs>
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87 <outputs>
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88 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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89 </outputs>
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90 <help><![CDATA[
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91 Balance Summary
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92 ###############
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93
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94 Visualize the distribution of a single balance and summarize its numerator
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95 and denominator components.
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96
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97 Parameters
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98 ----------
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99 table : FeatureTable[Frequency]
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100 A table of abundances.
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101 tree : Hierarchy
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102 The tree used to calculate the balances.
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103 taxonomy : FeatureData[Taxonomy]
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104 Taxonomy information for the OTUs.
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105 balance_name : Str
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106 Name of the balance to summarize.
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107 pseudocount : Float, optional
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108 The pseudocount to add to avoid division by zero.
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109 taxa_level : Int, optional
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110 Level of taxonomy to summarize.
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111 n_features : Int, optional
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112 The number of features to plot in the proportion plot.
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113 threshold : Float, optional
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114 A threshold to designate discrete categories for a numerical metadata
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115 column. This will split the numerical column values into two
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116 categories, values below the threshold, and values above the threshold.
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117 If not specified, this threshold will default to the mean.
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118 metadata : MetadataColumn[Categorical | Numeric], optional
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119 Metadata column for plotting the balance (optional).
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120
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121 Returns
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122 -------
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123 visualization : Visualization
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124 ]]></help>
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125 <macros>
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126 <import>qiime_citation.xml</import>
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127 </macros>
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128 <expand macro="qiime_citation"/>
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129 </tool>
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