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comparison qiime2/qiime_quality-control_evaluate-composition.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition"
3 version="2020.8">
4 <description>Evaluate expected vs. observed taxonomic composition of samples</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime quality-control evaluate-composition
10
11 --i-expected-features=$iexpectedfeatures
12
13 --i-observed-features=$iobservedfeatures
14
15 --p-depth=$pdepth
16
17 #if str($ppalette) != 'None':
18 --p-palette=$ppalette
19 #end if
20
21 #if $pnoplottar:
22 --p-no-plot-tar
23 #end if
24
25 #if $pnoplottdr:
26 --p-no-plot-tdr
27 #end if
28
29 #if $pplotrvalue:
30 --p-plot-r-value
31 #end if
32
33 #if $pnoplotrsquared:
34 --p-no-plot-r-squared
35 #end if
36
37 #if $pplotbraycurtis:
38 --p-plot-bray-curtis
39 #end if
40
41 #if $pplotjaccard:
42 --p-plot-jaccard
43 #end if
44
45 #if $pplotobservedfeatures:
46 --p-plot-observed-features
47 #end if
48
49 #if $pnoplotobservedfeaturesratio:
50 --p-no-plot-observed-features-ratio
51 #end if
52 # if $input_files_mmetadatafile:
53 # def list_dict_to_string(list_dict):
54 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
55 # for d in list_dict[1:]:
56 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
57 # end for
58 # return $file_list
59 # end def
60 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
61 # end if
62
63 #if '__ob__' in str($mmetadatacolumn):
64 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
65 #set $mmetadatacolumn = $mmetadatacolumn_temp
66 #end if
67 #if '__cb__' in str($mmetadatacolumn):
68 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
69 #set $mmetadatacolumn = $mmetadatacolumn_temp
70 #end if
71 #if 'X' in str($mmetadatacolumn):
72 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
73 #set $mmetadatacolumn = $mmetadatacolumn_temp
74 #end if
75 #if '__sq__' in str($mmetadatacolumn):
76 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
77 #set $mmetadatacolumn = $mmetadatacolumn_temp
78 #end if
79 #if '__db__' in str($mmetadatacolumn):
80 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
81 #set $mmetadatacolumn = $mmetadatacolumn_temp
82 #end if
83
84 #if str($mmetadatacolumn):
85 --m-metadata-column=$mmetadatacolumn
86 #end if
87
88 --o-visualization=ovisualization
89
90 #if str($examples) != 'None':
91 --examples=$examples
92 #end if
93
94 ;
95 cp odatabase.qza $odatabase
96
97 ;
98 qiime tools export ovisualization.qzv --output-path out
99 && mkdir -p '$ovisualization.files_path'
100 && cp -r out/* '$ovisualization.files_path'
101 && mv '$ovisualization.files_path/index.html' '$ovisualization'
102
103 ]]></command>
104 <inputs>
105 <param format="qza,no_unzip.zip" label="--i-expected-features: ARTIFACT FeatureTable[RelativeFrequency] Expected feature compositions [required]" name="iexpectedfeatures" optional="False" type="data" />
106 <param format="qza,no_unzip.zip" label="--i-observed-features: ARTIFACT FeatureTable[RelativeFrequency] Observed feature compositions [required]" name="iobservedfeatures" optional="False" type="data" />
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" />
108 <param label="--p-palette: " name="ppalette" optional="True" type="select">
109 <option selected="True" value="None">Selection is Optional</option>
110 <option value="Set1">Set1</option>
111 <option value="Set2">Set2</option>
112 <option value="Set3">Set3</option>
113 <option value="Pastel1">Pastel1</option>
114 <option value="Pastel2">Pastel2</option>
115 <option value="Paired">Paired</option>
116 <option value="Accent">Accent</option>
117 <option value="Dark2">Dark2</option>
118 <option value="tab10">tab10</option>
119 <option value="tab20">tab20</option>
120 <option value="tab20b">tab20b</option>
121 <option value="tab20c">tab20c</option>
122 <option value="viridis">viridis</option>
123 <option value="plasma">plasma</option>
124 <option value="inferno">inferno</option>
125 <option value="magma">magma</option>
126 <option value="terrain">terrain</option>
127 <option value="rainbow">rainbow</option>
128 </param>
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" />
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" />
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" />
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" />
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" />
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" />
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" />
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" />
137 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
138 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
139 </repeat>
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" />
141 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
142
143 </inputs>
144
145 <outputs>
146 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
147
148 </outputs>
149
150 <help><![CDATA[
151 Evaluate expected vs. observed taxonomic composition of samples
152 ###############################################################
153
154 This visualizer compares the feature composition of pairs of observed and
155 expected samples containing the same sample ID in two separate feature
156 tables. Typically, feature composition will consist of taxonomy
157 classifications or other semicolon-delimited feature annotations. Taxon
158 accuracy rate, taxon detection rate, and linear regression scores between
159 expected and observed observations are calculated at each semicolon-
160 delimited rank, and plots of per-level accuracy and observation
161 correlations are plotted. A histogram of distance between false positive
162 observations and the nearest expected feature is also generated, where
163 distance equals the number of rank differences between the observed feature
164 and the nearest common lineage in the expected feature. This visualizer is
165 most suitable for testing per-run data quality on sequencing runs that
166 contain mock communities or other samples with known composition. Also
167 suitable for sanity checks of bioinformatics pipeline performance.
168
169 Parameters
170 ----------
171 expected_features : FeatureTable[RelativeFrequency]
172 Expected feature compositions
173 observed_features : FeatureTable[RelativeFrequency]
174 Observed feature compositions
175 depth : Int, optional
176 Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
177 root, 7 = species for the greengenes reference sequence database).
178 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
179 Color palette to utilize for plotting.
180 plot_tar : Bool, optional
181 Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true
182 positive features divided by the total number of observed features (TAR
183 = true positives / (true positives + false positives)).
184 plot_tdr : Bool, optional
185 Plot taxon detection rate (TDR) on score plot. TDR is the number of
186 true positive features divided by the total number of expected features
187 (TDR = true positives / (true positives + false negatives)).
188 plot_r_value : Bool, optional
189 Plot expected vs. observed linear regression r value on score plot.
190 plot_r_squared : Bool, optional
191 Plot expected vs. observed linear regression r-squared value on score
192 plot.
193 plot_bray_curtis : Bool, optional
194 Plot expected vs. observed Bray-Curtis dissimilarity scores on score
195 plot.
196 plot_jaccard : Bool, optional
197 Plot expected vs. observed Jaccard distances scores on score plot.
198 plot_observed_features : Bool, optional
199 Plot observed features count on score plot.
200 plot_observed_features_ratio : Bool, optional
201 Plot ratio of observed:expected features on score plot.
202 metadata : MetadataColumn[Categorical], optional
203 Optional sample metadata that maps observed_features sample IDs to
204 expected_features sample IDs.
205
206 Returns
207 -------
208 visualization : Visualization
209 ]]></help>
210 <macros>
211 <import>qiime_citation.xml</import>
212 </macros>
213 <expand macro="qiime_citation"/>
214 </tool>