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comparison qiime2/qiime_quality-control_evaluate-composition.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -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="2019.4">
3 <description> - Evaluate expected vs. observed taxonomic composition of samples</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime quality-control evaluate-composition
9
10 --i-expected-features=$iexpectedfeatures
11 --i-observed-features=$iobservedfeatures
12
13 #if $input_files_mmetadatafile:
14 #def list_dict_to_string(list_dict):
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
16 #for d in list_dict[1:]:
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
18 #end for
19 #return $file_list
20 #end def
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 #end if
23
24
25 #if $pdepth:
26 --p-depth=$pdepth
27 #end if
28
29 #if str($ppalette) != 'None':
30 --p-palette=$ppalette
31 #end if
32
33 #if $pplottar:
34 --p-plot-tar
35 #end if
36
37 #if $pplottdr:
38 --p-plot-tdr
39 #end if
40
41 #if $pplotrvalue:
42 --p-plot-r-value
43 #end if
44
45 #if $pnoplotrsquared:
46 --p-no-plot-r-squared
47 #end if
48
49 #if $pplotbraycurtis:
50 --p-plot-bray-curtis
51 #end if
52
53 #if $pplotjaccard:
54 --p-plot-jaccard
55 #end if
56
57 #if $pplotobservedfeatures:
58 --p-plot-observed-features
59 #end if
60
61 #if $pplotobservedfeaturesratio:
62 --p-plot-observed-features-ratio
63 #end if
64
65 #if str($mmetadatacolumn):
66 --m-metadata-column="$mmetadatacolumn"
67 #end if
68
69 --o-visualization=ovisualization
70 ;
71 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
72 && cp -r out/* '$ovisualization.files_path'
73 && mv '$ovisualization.files_path/index.html' '$ovisualization'
74 ]]></command>
75 <inputs>
76 <param format="qza,no_unzip.zip" label="--i-expected-features: ARTIFACT FeatureTable[RelativeFrequency] Expected feature compositions [required]" name="iexpectedfeatures" optional="False" type="data"/>
77 <param format="qza,no_unzip.zip" label="--i-observed-features: ARTIFACT FeatureTable[RelativeFrequency] Observed feature compositions [required]" name="iobservedfeatures" optional="False" type="data"/>
78 <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"/>
79 <param label="--p-palette: " name="ppalette" optional="True" type="select">
80 <option selected="True" value="None">Selection is Optional</option>
81 <option value="Set1">Set1</option>
82 <option value="Set2">Set2</option>
83 <option value="Set3">Set3</option>
84 <option value="Pastel1">Pastel1</option>
85 <option value="Pastel2">Pastel2</option>
86 <option value="Paired">Paired</option>
87 <option value="Accent">Accent</option>
88 <option value="Dark2">Dark2</option>
89 <option value="tab10">tab10</option>
90 <option value="tab20">tab20</option>
91 <option value="tab20b">tab20b</option>
92 <option value="tab20c">tab20c</option>
93 <option value="viridis">viridis</option>
94 <option value="plasma">plasma</option>
95 <option value="inferno">inferno</option>
96 <option value="magma">magma</option>
97 <option value="terrain">terrain</option>
98 <option value="rainbow">rainbow</option>
99 </param>
100 <param label="--p-plot-tar: --p-no-plot-tar 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 " name="pplottar" selected="False" type="boolean"/>
101 <param label="--p-plot-tdr: --p-no-plot-tdr 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 " name="pplottdr" selected="False" type="boolean"/>
102 <param label="--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"/>
103 <param label="--p-no-plot-r-squared: Do not plot expected vs. observed linear regression r-squared value on score plot. [default: False]" name="pnoplotrsquared" selected="False" type="boolean"/>
104 <param label="--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"/>
105 <param label="--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"/>
106 <param label="--p-plot-observed-features: --p-no-plot-observed-features Plot observed features count on score plot. [default: False]" name="pplotobservedfeatures" selected="False" type="boolean"/>
107 <param label="--p-no-plot-observed-features-ratio: Do not plot ratio of observed:expected features on score plot. [default: False]" name="pnoplotobservedfeaturesratio" selected="False" type="boolean"/>
108 <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="True" type="text"/>
109
110 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
111 <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" />
112 </repeat>
113
114 </inputs>
115 <outputs>
116 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
117 </outputs>
118 <help><![CDATA[
119 Evaluate expected vs. observed taxonomic composition of samples
120 ###############################################################
121
122 This visualizer compares the feature composition of pairs of observed and
123 expected samples containing the same sample ID in two separate feature
124 tables. Typically, feature composition will consist of taxonomy
125 classifications or other semicolon-delimited feature annotations. Taxon
126 accuracy rate, taxon detection rate, and linear regression scores between
127 expected and observed observations are calculated at each semicolon-
128 delimited rank, and plots of per-level accuracy and observation
129 correlations are plotted. A histogram of distance between false positive
130 observations and the nearest expected feature is also generated, where
131 distance equals the number of rank differences between the observed feature
132 and the nearest common lineage in the expected feature. This visualizer is
133 most suitable for testing per-run data quality on sequencing runs that
134 contain mock communities or other samples with known composition. Also
135 suitable for sanity checks of bioinformatics pipeline performance.
136
137 Parameters
138 ----------
139 expected_features : FeatureTable[RelativeFrequency]
140 Expected feature compositions
141 observed_features : FeatureTable[RelativeFrequency]
142 Observed feature compositions
143 depth : Int, optional
144 Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
145 root, 7 = species for the greengenes reference sequence database).
146 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
147 Color palette to utilize for plotting.
148 plot_tar : Bool, optional
149 Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true
150 positive features divided by the total number of observed features (TAR
151 = true positives / (true positives + false positives)).
152 plot_tdr : Bool, optional
153 Plot taxon detection rate (TDR) on score plot. TDR is the number of
154 true positive features divided by the total number of expected features
155 (TDR = true positives / (true positives + false negatives)).
156 plot_r_value : Bool, optional
157 Plot expected vs. observed linear regression r value on score plot.
158 plot_r_squared : Bool, optional
159 Plot expected vs. observed linear regression r-squared value on score
160 plot.
161 plot_bray_curtis : Bool, optional
162 Plot expected vs. observed Bray-Curtis dissimilarity scores on score
163 plot.
164 plot_jaccard : Bool, optional
165 Plot expected vs. observed Jaccard distances scores on score plot.
166 plot_observed_features : Bool, optional
167 Plot observed features count on score plot.
168 plot_observed_features_ratio : Bool, optional
169 Plot ratio of observed:expected features on score plot.
170 metadata : MetadataColumn[Categorical], optional
171 Optional sample metadata that maps observed_features sample IDs to
172 expected_features sample IDs.
173
174 Returns
175 -------
176 visualization : Visualization
177 ]]></help>
178 <macros>
179 <import>qiime_citation.xml</import>
180 </macros>
181 <expand macro="qiime_citation"/>
182 </tool>