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1 <?xml version="1.0" ?>
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2 <tool id="qiime_quality-control_evaluate-taxonomy" name="qiime quality-control evaluate-taxonomy"
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3 version="2020.8">
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4 <description>Evaluate expected vs. observed taxonomic assignments</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 quality-control evaluate-taxonomy
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10
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11 --i-expected-taxa=$iexpectedtaxa
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12
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13 --i-observed-taxa=$iobservedtaxa
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6
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15 #if $ifeaturetable:
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16 --i-feature-table
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17 #end if
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18
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19 --p-depth=$pdepth
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20
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21 #if str($ppalette) != 'None':
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22 --p-palette=$ppalette
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23 #end if
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24
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25 #if $pnorequireexpids:
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26 --p-no-require-exp-ids
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27 #end if
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28
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29 #if $pnorequireobsids:
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30 --p-no-require-obs-ids
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31 #end if
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32
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33 #if str($psampleid):
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34 --p-sample-id=$psampleid
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35 #end if
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36 --o-visualization=ovisualization
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37
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38 #if str($examples) != 'None':
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39 --examples=$examples
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40 #end if
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41
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42 ;
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43 cp odatabase.qza $odatabase
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44
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45 ;
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46 qiime tools export ovisualization.qzv --output-path out
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47 && mkdir -p '$ovisualization.files_path'
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48 && cp -r out/* '$ovisualization.files_path'
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49 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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50
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51 ;
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52 qiime tools export ovisualization.qzv --output-path out
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53 && mkdir -p '$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' '$ovisualization'
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56
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57 ;
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58 qiime tools export ovisualization.qzv --output-path out
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59 && mkdir -p '$ovisualization.files_path'
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60 && cp -r out/* '$ovisualization.files_path'
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61 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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62
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63 ]]></command>
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64 <inputs>
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65 <param format="qza,no_unzip.zip" label="--i-expected-taxa: ARTIFACT FeatureData[Taxonomy] Expected taxonomic assignments [required]" name="iexpectedtaxa" optional="False" type="data" />
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66 <param format="qza,no_unzip.zip" label="--i-observed-taxa: ARTIFACT FeatureData[Taxonomy] Observed taxonomic assignments [required]" name="iobservedtaxa" optional="False" type="data" />
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67 <param format="qza,no_unzip.zip" label="--i-feature-table: --i-feature-table: ARTIFACT FeatureTable[RelativeFrequency] Optional feature table containing relative frequency of each feature, used to weight accuracy scores by frequency. Must contain all features found in expected and/or observed taxa. Features found in the table but not the expected/observed taxa will be dropped prior to analysis. [optional]" name="ifeaturetable" selected="False" type="boolean" />
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68 <param label="--p-depth: INTEGER Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [required]" name="pdepth" optional="False" type="text" />
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69 <param label="--p-palette: " name="ppalette" optional="True" type="select">
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70 <option selected="True" value="None">Selection is Optional</option>
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71 <option value="Set1">Set1</option>
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72 <option value="Set2">Set2</option>
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73 <option value="Set3">Set3</option>
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74 <option value="Pastel1">Pastel1</option>
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75 <option value="Pastel2">Pastel2</option>
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76 <option value="Paired">Paired</option>
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77 <option value="Accent">Accent</option>
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78 <option value="Dark2">Dark2</option>
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79 <option value="tab10">tab10</option>
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80 <option value="tab20">tab20</option>
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81 <option value="tab20b">tab20b</option>
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82 <option value="tab20c">tab20c</option>
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83 <option value="viridis">viridis</option>
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84 <option value="plasma">plasma</option>
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85 <option value="inferno">inferno</option>
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86 <option value="magma">magma</option>
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87 <option value="terrain">terrain</option>
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88 <option value="rainbow">rainbow</option>
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89 </param>
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90 <param label="--p-no-require-exp-ids: Do not require that all features found in observed taxa must be found in expected taxa or raise error. [default: True]" name="pnorequireexpids" selected="False" type="boolean" />
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91 <param label="--p-no-require-obs-ids: Do not require that all features found in expected taxa must be found in observed taxa or raise error. [default: True]" name="pnorequireobsids" selected="False" type="boolean" />
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92 <param label="--p-sample-id: TEXT Optional sample ID to use for extracting frequency data from feature table, and for labeling accuracy results. If no sample-id is provided, feature frequencies are derived from the sum of all samples present in the feature table. [optional]" name="psampleid" optional="False" type="text" />
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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 Evaluate expected vs. observed taxonomic assignments
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104 ###############################################################
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105
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106 This visualizer compares a pair of observed and expected taxonomic
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107 assignments to calculate precision, recall, and F-measure at each taxonomic
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108 level, up to maximum level specified by the depth parameter. These metrics
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109 are calculated at each semicolon-delimited rank. This action is useful for
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110 comparing the accuracy of taxonomic assignment, e.g., between different
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111 taxonomy classifiers or other bioinformatics methods. Expected taxonomies
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112 should be derived from simulated or mock community sequences that have
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113 known taxonomic affiliations.
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114
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115 Parameters
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116 ----------
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117 expected_taxa : FeatureData[Taxonomy]
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118 Expected taxonomic assignments
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119 observed_taxa : FeatureData[Taxonomy]
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120 Observed taxonomic assignments
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121 depth : Int
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122 Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
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123 root, 7 = species for the greengenes reference sequence database).
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124 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
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125 Color palette to utilize for plotting.
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126 require_exp_ids : Bool, optional
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127 Require that all features found in observed taxa must be found in
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128 expected taxa or raise error.
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129 require_obs_ids : Bool, optional
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130 Require that all features found in expected taxa must be found in
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131 observed taxa or raise error.
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132 feature_table : FeatureTable[RelativeFrequency], optional
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133 Optional feature table containing relative frequency of each feature,
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134 used to weight accuracy scores by frequency. Must contain all features
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135 found in expected and/or observed taxa. Features found in the table but
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136 not the expected/observed taxa will be dropped prior to analysis.
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137 sample_id : Str, optional
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138 Optional sample ID to use for extracting frequency data from feature
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139 table, and for labeling accuracy results. If no sample_id is provided,
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140 feature frequencies are derived from the sum of all samples present in
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141 the feature table.
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142
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143 Returns
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144 -------
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145 visualization : Visualization
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146 ]]></help>
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147 <macros>
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148 <import>qiime_citation.xml</import>
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149 </macros>
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150 <expand macro="qiime_citation"/>
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151 </tool> |
