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1 <?xml version="1.0" ?>
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2 <tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition" version="2018.4">
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3 <description> - Evaluate expected vs. observed taxonomic composition of samples</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>
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8 <![CDATA[
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9 qiime quality-control evaluate-composition --i-expected-features=$iexpectedfeatures --i-observed-features=$iobservedfeatures
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10
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11 #if $input_files_mmetadatafile:
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12
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13 #def list_dict_to_string(list_dict):
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14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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15 #for d in list_dict[1:]:
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16 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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17 #end for
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18 #return $file_list
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19 #end def
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20
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21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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22 #end if
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23
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24 #if str($cmdconfig) != 'None':
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25 --cmd-config=$cmdconfig
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26 #end if
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27
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28 #if $pplotrvalue:
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29 --p-plot-r-value
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30 #else
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31 --p-no-plot-r-value
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32 #end if
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33
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34 #if str($mmetadatacolumn):
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35 --m-metadata-column="$mmetadatacolumn"
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36 #end if
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37
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38 #if $pplotrsquared:
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39 --p-plot-r-squared
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40 #else
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41 --p-no-plot-r-squared
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42 #end if
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43
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44 #if $pdepth:
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45 --p-depth=$pdepth
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46 #end if
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47
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48 #if $pplottar:
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49 --p-plot-tar
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50 #else
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51 --p-no-plot-tar
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52 #end if
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53
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54 #if $pplotobservedfeaturesratio:
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55 --p-plot-observed-features-ratio
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56 #else
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57 --p-no-plot-observed-features-ratio
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58 #end if
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59
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60 #if str($ppalette) != 'None':
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61 --p-palette=$ppalette
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62 #end if
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63
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64 #if $pplottdr:
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65 --p-plot-tdr
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66 #else
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67 --p-no-plot-tdr
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68 #end if
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69 --o-visualization=ovisualization
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70 #if $pplotobservedfeatures:
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71 --p-plot-observed-features
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72 #else
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73 --p-no-plot-observed-features
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74 #end if
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75 ;
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76 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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77 && cp -r out/* '$ovisualization.files_path'
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78 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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79 ]]>
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80 </command>
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81 <inputs>
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82 <param format="qza,no_unzip.zip" label="--i-expected-features: FeatureTable[RelativeFrequency] Expected feature compositions [required]" name="iexpectedfeatures" optional="False" type="data"/>
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83 <param format="qza,no_unzip.zip" label="--i-observed-features: FeatureTable[RelativeFrequency] Observed feature compositions [required]" name="iobservedfeatures" optional="False" type="data"/>
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84
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85 <param label="--p-depth: Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [default: 7]" name="pdepth" optional="True" type="integer" value="7"/>
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86
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87 <param label="--p-palette: Color palette to utilize for plotting.[default: Set1]" name="ppalette" optional="True" type="select">
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88 <option selected="True" value="None">Selection is Optional</option>
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89 <option value="Accent">Accent</option>
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90 <option value="tab20">tab20</option>
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91 <option value="Pastel2">Pastel2</option>
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92 <option value="plasma">plasma</option>
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93 <option value="viridis">viridis</option>
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94 <option value="rainbow">rainbow</option>
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95 <option value="Pastel1">Pastel1</option>
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96 <option value="inferno">inferno</option>
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97 <option value="magma">magma</option>
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98 <option value="tab20b">tab20b</option>
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99 <option value="Set3">Set3</option>
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100 <option value="Set2">Set2</option>
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101 <option value="Dark2">Dark2</option>
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102 <option value="Set1">Set1</option>
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103 <option value="tab10">tab10</option>
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104 <option value="tab20c">tab20c</option>
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105 <option value="terrain">terrain</option>
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106 <option value="Paired">Paired</option>
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107 </param>
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108
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109
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110 <param label="--p-plot-tar / --p-no-plot-tar Plot taxon accuracy rate (TAR) on score
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111 plot. TAR is the number of true positive
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112 features divided by the total number of
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113 observed features (TAR = true positives
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114 (true positives + false positives)).
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115 [default: True]" name="pplottar" checked="True" type="boolean"/>
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116 <param label="--p-plot-tdr / --p-no-plot-tdr Plot taxon detection rate (TDR) on score
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117 plot. TDR is the number of true positive
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118 features divided by the total number of
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119 expected features (TDR = true positives
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120 (true positives + false negatives)).
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121 [default: True]" name="pplottdr" checked="True" type="boolean"/>
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122 <param label="--p-plot-r-value / --p-no-plot-r-value
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123 Plot expected vs. observed linear regression
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124 r value on score plot. [default: False]" name="pplotrvalue" checked="False" type="boolean"/>
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125 <param label="--p-plot-r-squared / --p-no-plot-r-squared
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126 Plot expected vs. observed linear regression
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127 r-squared value on score plot. [default:
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128 True]" name="pplotrsquared" checked="True" type="boolean"/>
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129
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130 <param label="--p-plot-observed-features / --p-no-plot-observed-features
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131 Plot observed features count on score plot.
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132 [default: False]" name="pplotobservedfeatures" checked="False" type="boolean"/>
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133 <param label="--p-plot-observed-features-ratio / --p-no-plot-observed-features-ratio
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134 Plot ratio of observed:expected features on
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135 score plot. [default: True]" name="pplotobservedfeaturesratio" checked="True" type="boolean"/>
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136
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137 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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138 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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139 </repeat>
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140 <param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. Optional sample metadata that maps observed_features sample IDs to expected_features sample IDs. [optional]" name="mmetadatacolumn" optional="True" type="text"/>
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141
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142 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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143 </inputs>
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144 <outputs>
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145 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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146 </outputs>
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147 <help>
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148 <![CDATA[
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149 Evaluate expected vs. observed taxonomic composition of samples
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150 ----------------------------------------------------------------
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151
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152 This visualizer compares the feature composition of pairs of observed and
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153 expected samples containing the same sample ID in two separate feature
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154 tables. Typically, feature composition will consist of taxonomy
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155 classifications or other semicolon-delimited feature annotations. Taxon
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156 accuracy rate, taxon detection rate, and linear regression scores between
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157 expected and observed observations are calculated at each semicolon-
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158 delimited rank, and plots of per-level accuracy and observation
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159 correlations are plotted. A histogram of distance between false positive
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160 observations and the nearest expected feature is also generated, where
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161 distance equals the number of rank differences between the observed feature
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162 and the nearest common lineage in the expected feature. This visualizer is
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163 most suitable for testing per-run data quality on sequencing runs that
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164 contain mock communities or other samples with known composition. Also
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165 suitable for sanity checks of bioinformatics pipeline performance.
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166
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167 Parameters
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168 ----------
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169 expected_features : FeatureTable[RelativeFrequency]
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170 Expected feature compositions
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171 observed_features : FeatureTable[RelativeFrequency]
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172 Observed feature compositions
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173 depth : Int, optional
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174 Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
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175 root, 7 = species for the greengenes reference sequence database).
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176 palette : Str % Choices({'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'inferno', 'magma', 'plasma', 'rainbow', 'tab10', 'tab20', 'tab20b', 'tab20c', 'terrain', 'viridis'}), optional
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177 Color palette to utilize for plotting.
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178 plot_tar : Bool, optional
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179 Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true
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180 positive features divided by the total number of observed features (TAR
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181 = true positives / (true positives + false positives)).
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182 plot_tdr : Bool, optional
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183 Plot taxon detection rate (TDR) on score plot. TDR is the number of
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184 true positive features divided by the total number of expected features
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185 (TDR = true positives / (true positives + false negatives)).
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186 plot_r_value : Bool, optional
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187 Plot expected vs. observed linear regression r value on score plot.
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188 plot_r_squared : Bool, optional
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189 Plot expected vs. observed linear regression r-squared value on score
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190 plot.
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191 plot_observed_features : Bool, optional
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192 Plot observed features count on score plot.
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193 plot_observed_features_ratio : Bool, optional
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194 Plot ratio of observed:expected features on score plot.
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195 metadata : MetadataColumn[Categorical], optional
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196 Optional sample metadata that maps observed_features sample IDs to
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197 expected_features sample IDs.
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198
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199 Returns
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200 -------
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201 visualization : Visualization
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202 \
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203 ]]>
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204 </help>
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205 </tool>
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