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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"
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3 version="2020.8">
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4 <description>Evaluate expected vs. observed taxonomic composition of samples</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-composition
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10
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11 --i-expected-features=$iexpectedfeatures
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12
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13 --i-observed-features=$iobservedfeatures
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14
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15 --p-depth=$pdepth
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16
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17 #if str($ppalette) != 'None':
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18 --p-palette=$ppalette
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19 #end if
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20
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21 #if $pnoplottar:
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22 --p-no-plot-tar
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23 #end if
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24
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25 #if $pnoplottdr:
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26 --p-no-plot-tdr
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27 #end if
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28
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29 #if $pplotrvalue:
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30 --p-plot-r-value
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31 #end if
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32
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33 #if $pnoplotrsquared:
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34 --p-no-plot-r-squared
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35 #end if
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36
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37 #if $pplotbraycurtis:
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38 --p-plot-bray-curtis
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39 #end if
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40
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41 #if $pplotjaccard:
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42 --p-plot-jaccard
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43 #end if
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44
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45 #if $pplotobservedfeatures:
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46 --p-plot-observed-features
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47 #end if
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48
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49 #if $pnoplotobservedfeaturesratio:
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50 --p-no-plot-observed-features-ratio
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51 #end if
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52 # if $input_files_mmetadatafile:
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53 # def list_dict_to_string(list_dict):
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54 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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55 # for d in list_dict[1:]:
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56 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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57 # end for
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58 # return $file_list
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59 # end def
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60 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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61 # end if
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62
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63 #if '__ob__' in str($mmetadatacolumn):
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64 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
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65 #set $mmetadatacolumn = $mmetadatacolumn_temp
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66 #end if
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67 #if '__cb__' in str($mmetadatacolumn):
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68 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
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69 #set $mmetadatacolumn = $mmetadatacolumn_temp
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70 #end if
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71 #if 'X' in str($mmetadatacolumn):
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72 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
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73 #set $mmetadatacolumn = $mmetadatacolumn_temp
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74 #end if
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75 #if '__sq__' in str($mmetadatacolumn):
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76 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
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77 #set $mmetadatacolumn = $mmetadatacolumn_temp
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78 #end if
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79 #if '__db__' in str($mmetadatacolumn):
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80 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
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81 #set $mmetadatacolumn = $mmetadatacolumn_temp
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82 #end if
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83
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84 #if str($mmetadatacolumn):
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85 --m-metadata-column=$mmetadatacolumn
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86 #end if
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87
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88 --o-visualization=ovisualization
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89
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90 #if str($examples) != 'None':
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91 --examples=$examples
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92 #end if
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93
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94 ;
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95 cp odatabase.qza $odatabase
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96
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97 ;
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98 qiime tools export ovisualization.qzv --output-path out
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99 && mkdir -p '$ovisualization.files_path'
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100 && cp -r out/* '$ovisualization.files_path'
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101 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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102
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103 ]]></command>
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104 <inputs>
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105 <param format="qza,no_unzip.zip" label="--i-expected-features: ARTIFACT FeatureTable[RelativeFrequency] Expected feature compositions [required]" name="iexpectedfeatures" optional="False" type="data" />
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106 <param format="qza,no_unzip.zip" label="--i-observed-features: ARTIFACT FeatureTable[RelativeFrequency] Observed feature compositions [required]" name="iobservedfeatures" optional="False" type="data" />
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107 <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). [default: 7]" name="pdepth" optional="True" type="integer" value="7" />
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108 <param label="--p-palette: " name="ppalette" optional="True" type="select">
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109 <option selected="True" value="None">Selection is Optional</option>
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110 <option value="Set1">Set1</option>
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111 <option value="Set2">Set2</option>
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112 <option value="Set3">Set3</option>
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113 <option value="Pastel1">Pastel1</option>
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114 <option value="Pastel2">Pastel2</option>
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115 <option value="Paired">Paired</option>
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116 <option value="Accent">Accent</option>
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117 <option value="Dark2">Dark2</option>
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118 <option value="tab10">tab10</option>
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119 <option value="tab20">tab20</option>
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120 <option value="tab20b">tab20b</option>
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121 <option value="tab20c">tab20c</option>
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122 <option value="viridis">viridis</option>
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123 <option value="plasma">plasma</option>
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124 <option value="inferno">inferno</option>
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125 <option value="magma">magma</option>
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126 <option value="terrain">terrain</option>
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127 <option value="rainbow">rainbow</option>
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128 </param>
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129 <param label="--p-no-plot-tar: Do not plot taxon accuracy rate (TAR) on score plot. TAR is the number of true positive features divided by the total number of observed features (TAR = true positives / (true positives + false positives)). [default: True]" name="pnoplottar" selected="False" type="boolean" />
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130 <param label="--p-no-plot-tdr: Do not plot taxon detection rate (TDR) on score plot. TDR is the number of true positive features divided by the total number of expected features (TDR = true positives / (true positives + false negatives)). [default: True]" name="pnoplottdr" selected="False" type="boolean" />
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131 <param label="--p-plot-r-value: --p-plot-r-value: / --p-no-plot-r-value Plot expected vs. observed linear regression r value on score plot. [default: False]" name="pplotrvalue" selected="False" type="boolean" />
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132 <param label="--p-no-plot-r-squared: Do not plot expected vs. observed linear regression r-squared value on score plot. [default: True]" name="pnoplotrsquared" selected="False" type="boolean" />
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133 <param label="--p-plot-bray-curtis: --p-plot-bray-curtis: / --p-no-plot-bray-curtis Plot expected vs. observed Bray-Curtis dissimilarity scores on score plot. [default: False]" name="pplotbraycurtis" selected="False" type="boolean" />
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134 <param label="--p-plot-jaccard: --p-plot-jaccard: / --p-no-plot-jaccard Plot expected vs. observed Jaccard distances scores on score plot. [default: False]" name="pplotjaccard" selected="False" type="boolean" />
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135 <param label="--p-plot-observed-features: --p-plot-observed-features: / --p-no-plot-observed-features Plot observed features count on score plot. [default: False]" name="pplotobservedfeatures" selected="False" type="boolean" />
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136 <param label="--p-no-plot-observed-features-ratio: Do not plot ratio of observed:expected features on score plot. [default: True]" name="pnoplotobservedfeaturesratio" selected="False" type="boolean" />
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137 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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138 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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139 </repeat>
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140 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs. [optional]" name="mmetadatacolumn" optional="False" type="text" />
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141 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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142
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143 </inputs>
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144
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145 <outputs>
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146 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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147
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148 </outputs>
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149
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150 <help><![CDATA[
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151 Evaluate expected vs. observed taxonomic composition of samples
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152 ###############################################################
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153
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154 This visualizer compares the feature composition of pairs of observed and
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155 expected samples containing the same sample ID in two separate feature
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156 tables. Typically, feature composition will consist of taxonomy
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157 classifications or other semicolon-delimited feature annotations. Taxon
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158 accuracy rate, taxon detection rate, and linear regression scores between
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159 expected and observed observations are calculated at each semicolon-
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160 delimited rank, and plots of per-level accuracy and observation
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161 correlations are plotted. A histogram of distance between false positive
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162 observations and the nearest expected feature is also generated, where
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163 distance equals the number of rank differences between the observed feature
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164 and the nearest common lineage in the expected feature. This visualizer is
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165 most suitable for testing per-run data quality on sequencing runs that
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166 contain mock communities or other samples with known composition. Also
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167 suitable for sanity checks of bioinformatics pipeline performance.
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168
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169 Parameters
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170 ----------
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171 expected_features : FeatureTable[RelativeFrequency]
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172 Expected feature compositions
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173 observed_features : FeatureTable[RelativeFrequency]
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174 Observed feature compositions
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175 depth : Int, optional
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176 Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
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177 root, 7 = species for the greengenes reference sequence database).
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178 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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179 Color palette to utilize for plotting.
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180 plot_tar : Bool, optional
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181 Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true
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182 positive features divided by the total number of observed features (TAR
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183 = true positives / (true positives + false positives)).
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184 plot_tdr : Bool, optional
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185 Plot taxon detection rate (TDR) on score plot. TDR is the number of
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186 true positive features divided by the total number of expected features
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187 (TDR = true positives / (true positives + false negatives)).
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188 plot_r_value : Bool, optional
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189 Plot expected vs. observed linear regression r value on score plot.
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190 plot_r_squared : Bool, optional
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191 Plot expected vs. observed linear regression r-squared value on score
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192 plot.
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193 plot_bray_curtis : Bool, optional
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194 Plot expected vs. observed Bray-Curtis dissimilarity scores on score
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195 plot.
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196 plot_jaccard : Bool, optional
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197 Plot expected vs. observed Jaccard distances scores on score plot.
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198 plot_observed_features : Bool, optional
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199 Plot observed features count on score plot.
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200 plot_observed_features_ratio : Bool, optional
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201 Plot ratio of observed:expected features on score plot.
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202 metadata : MetadataColumn[Categorical], optional
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203 Optional sample metadata that maps observed_features sample IDs to
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204 expected_features sample IDs.
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205
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206 Returns
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207 -------
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208 visualization : Visualization
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209 ]]></help>
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210 <macros>
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211 <import>qiime_citation.xml</import>
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212 </macros>
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213 <expand macro="qiime_citation"/>
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214 </tool> |
