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comparison qiime2/qiime_quality-control_evaluate-composition.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition" version="2018.4">
3 <description> - Evaluate expected vs. observed taxonomic composition of samples</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime quality-control evaluate-composition --i-expected-features=$iexpectedfeatures --i-observed-features=$iobservedfeatures
10
11 #if $input_files_mmetadatafile:
12
13 #def list_dict_to_string(list_dict):
14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 #for d in list_dict[1:]:
16 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 #end for
18 #return $file_list
19 #end def
20
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 #end if
23
24 #if str($cmdconfig) != 'None':
25 --cmd-config=$cmdconfig
26 #end if
27
28 #if $pplotrvalue:
29 --p-plot-r-value
30 #else
31 --p-no-plot-r-value
32 #end if
33
34 #if str($mmetadatacolumn):
35 --m-metadata-column="$mmetadatacolumn"
36 #end if
37
38 #if $pplotrsquared:
39 --p-plot-r-squared
40 #else
41 --p-no-plot-r-squared
42 #end if
43
44 #if $pdepth:
45 --p-depth=$pdepth
46 #end if
47
48 #if $pplottar:
49 --p-plot-tar
50 #else
51 --p-no-plot-tar
52 #end if
53
54 #if $pplotobservedfeaturesratio:
55 --p-plot-observed-features-ratio
56 #else
57 --p-no-plot-observed-features-ratio
58 #end if
59
60 #if str($ppalette) != 'None':
61 --p-palette=$ppalette
62 #end if
63
64 #if $pplottdr:
65 --p-plot-tdr
66 #else
67 --p-no-plot-tdr
68 #end if
69 --o-visualization=ovisualization
70 #if $pplotobservedfeatures:
71 --p-plot-observed-features
72 #else
73 --p-no-plot-observed-features
74 #end if
75 ;
76 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
77 && cp -r out/* '$ovisualization.files_path'
78 && mv '$ovisualization.files_path/index.html' '$ovisualization'
79 ]]>
80 </command>
81 <inputs>
82 <param format="qza,no_unzip.zip" label="--i-expected-features: FeatureTable[RelativeFrequency] Expected feature compositions [required]" name="iexpectedfeatures" optional="False" type="data"/>
83 <param format="qza,no_unzip.zip" label="--i-observed-features: FeatureTable[RelativeFrequency] Observed feature compositions [required]" name="iobservedfeatures" optional="False" type="data"/>
84
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"/>
86
87 <param label="--p-palette: Color palette to utilize for plotting.[default: Set1]" name="ppalette" optional="True" type="select">
88 <option selected="True" value="None">Selection is Optional</option>
89 <option value="Accent">Accent</option>
90 <option value="tab20">tab20</option>
91 <option value="Pastel2">Pastel2</option>
92 <option value="plasma">plasma</option>
93 <option value="viridis">viridis</option>
94 <option value="rainbow">rainbow</option>
95 <option value="Pastel1">Pastel1</option>
96 <option value="inferno">inferno</option>
97 <option value="magma">magma</option>
98 <option value="tab20b">tab20b</option>
99 <option value="Set3">Set3</option>
100 <option value="Set2">Set2</option>
101 <option value="Dark2">Dark2</option>
102 <option value="Set1">Set1</option>
103 <option value="tab10">tab10</option>
104 <option value="tab20c">tab20c</option>
105 <option value="terrain">terrain</option>
106 <option value="Paired">Paired</option>
107 </param>
108
109
110 <param label="--p-plot-tar / --p-no-plot-tar Plot taxon accuracy rate (TAR) on score
111 plot. TAR is the number of true positive
112 features divided by the total number of
113 observed features (TAR = true positives
114 (true positives + false positives)).
115 [default: True]" name="pplottar" checked="True" type="boolean"/>
116 <param label="--p-plot-tdr / --p-no-plot-tdr Plot taxon detection rate (TDR) on score
117 plot. TDR is the number of true positive
118 features divided by the total number of
119 expected features (TDR = true positives
120 (true positives + false negatives)).
121 [default: True]" name="pplottdr" checked="True" type="boolean"/>
122 <param label="--p-plot-r-value / --p-no-plot-r-value
123 Plot expected vs. observed linear regression
124 r value on score plot. [default: False]" name="pplotrvalue" checked="False" type="boolean"/>
125 <param label="--p-plot-r-squared / --p-no-plot-r-squared
126 Plot expected vs. observed linear regression
127 r-squared value on score plot. [default:
128 True]" name="pplotrsquared" checked="True" type="boolean"/>
129
130 <param label="--p-plot-observed-features / --p-no-plot-observed-features
131 Plot observed features count on score plot.
132 [default: False]" name="pplotobservedfeatures" checked="False" type="boolean"/>
133 <param label="--p-plot-observed-features-ratio / --p-no-plot-observed-features-ratio
134 Plot ratio of observed:expected features on
135 score plot. [default: True]" name="pplotobservedfeaturesratio" checked="True" type="boolean"/>
136
137 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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" />
139 </repeat>
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"/>
141
142 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
143 </inputs>
144 <outputs>
145 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
146 </outputs>
147 <help>
148 <![CDATA[
149 Evaluate expected vs. observed taxonomic composition of samples
150 ----------------------------------------------------------------
151
152 This visualizer compares the feature composition of pairs of observed and
153 expected samples containing the same sample ID in two separate feature
154 tables. Typically, feature composition will consist of taxonomy
155 classifications or other semicolon-delimited feature annotations. Taxon
156 accuracy rate, taxon detection rate, and linear regression scores between
157 expected and observed observations are calculated at each semicolon-
158 delimited rank, and plots of per-level accuracy and observation
159 correlations are plotted. A histogram of distance between false positive
160 observations and the nearest expected feature is also generated, where
161 distance equals the number of rank differences between the observed feature
162 and the nearest common lineage in the expected feature. This visualizer is
163 most suitable for testing per-run data quality on sequencing runs that
164 contain mock communities or other samples with known composition. Also
165 suitable for sanity checks of bioinformatics pipeline performance.
166
167 Parameters
168 ----------
169 expected_features : FeatureTable[RelativeFrequency]
170 Expected feature compositions
171 observed_features : FeatureTable[RelativeFrequency]
172 Observed feature compositions
173 depth : Int, optional
174 Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
175 root, 7 = species for the greengenes reference sequence database).
176 palette : Str % Choices({'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'inferno', 'magma', 'plasma', 'rainbow', 'tab10', 'tab20', 'tab20b', 'tab20c', 'terrain', 'viridis'}), optional
177 Color palette to utilize for plotting.
178 plot_tar : Bool, optional
179 Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true
180 positive features divided by the total number of observed features (TAR
181 = true positives / (true positives + false positives)).
182 plot_tdr : Bool, optional
183 Plot taxon detection rate (TDR) on score plot. TDR is the number of
184 true positive features divided by the total number of expected features
185 (TDR = true positives / (true positives + false negatives)).
186 plot_r_value : Bool, optional
187 Plot expected vs. observed linear regression r value on score plot.
188 plot_r_squared : Bool, optional
189 Plot expected vs. observed linear regression r-squared value on score
190 plot.
191 plot_observed_features : Bool, optional
192 Plot observed features count on score plot.
193 plot_observed_features_ratio : Bool, optional
194 Plot ratio of observed:expected features on score plot.
195 metadata : MetadataColumn[Categorical], optional
196 Optional sample metadata that maps observed_features sample IDs to
197 expected_features sample IDs.
198
199 Returns
200 -------
201 visualization : Visualization
202 \
203 ]]>
204 </help>
205 <macros>
206 <import>qiime_citation.xml</import>
207 </macros>
208 <expand macro="qiime_citation" />
209 </tool>