|
29
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Plot longitudinal feature volatility and importances</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime longitudinal plot-feature-volatility
|
|
|
10
|
|
|
11 --i-table=$itable
|
|
|
12
|
|
|
13 --i-importances=$iimportances
|
|
|
14 # if $input_files_mmetadatafile:
|
|
|
15 # def list_dict_to_string(list_dict):
|
|
|
16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
17 # for d in list_dict[1:]:
|
|
|
18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
|
19 # end for
|
|
|
20 # return $file_list
|
|
|
21 # end def
|
|
|
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
|
23 # end if
|
|
|
24
|
|
|
25 #if '__ob__' in str($pstatecolumn):
|
|
|
26 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
|
|
|
27 #set $pstatecolumn = $pstatecolumn_temp
|
|
|
28 #end if
|
|
|
29 #if '__cb__' in str($pstatecolumn):
|
|
|
30 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
|
|
|
31 #set $pstatecolumn = $pstatecolumn_temp
|
|
|
32 #end if
|
|
|
33 #if 'X' in str($pstatecolumn):
|
|
|
34 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
|
|
|
35 #set $pstatecolumn = $pstatecolumn_temp
|
|
|
36 #end if
|
|
|
37 #if '__sq__' in str($pstatecolumn):
|
|
|
38 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
|
|
|
39 #set $pstatecolumn = $pstatecolumn_temp
|
|
|
40 #end if
|
|
|
41 #if '__db__' in str($pstatecolumn):
|
|
|
42 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
|
|
|
43 #set $pstatecolumn = $pstatecolumn_temp
|
|
|
44 #end if
|
|
|
45
|
|
|
46 --p-state-column=$pstatecolumn
|
|
|
47
|
|
|
48
|
|
|
49 #if '__ob__' in str($pindividualidcolumn):
|
|
|
50 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
|
|
|
51 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
52 #end if
|
|
|
53 #if '__cb__' in str($pindividualidcolumn):
|
|
|
54 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
|
|
|
55 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
56 #end if
|
|
|
57 #if 'X' in str($pindividualidcolumn):
|
|
|
58 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
|
|
|
59 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
60 #end if
|
|
|
61 #if '__sq__' in str($pindividualidcolumn):
|
|
|
62 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
|
|
|
63 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
64 #end if
|
|
|
65 #if '__db__' in str($pindividualidcolumn):
|
|
|
66 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
|
|
|
67 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
68 #end if
|
|
|
69
|
|
|
70 #if str($pindividualidcolumn):
|
|
|
71 --p-individual-id-column=$pindividualidcolumn
|
|
|
72 #end if
|
|
|
73
|
|
|
74 #if '__ob__' in str($pdefaultgroupcolumn):
|
|
|
75 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__ob__', '[')
|
|
|
76 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
|
|
|
77 #end if
|
|
|
78 #if '__cb__' in str($pdefaultgroupcolumn):
|
|
|
79 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__cb__', ']')
|
|
|
80 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
|
|
|
81 #end if
|
|
|
82 #if 'X' in str($pdefaultgroupcolumn):
|
|
|
83 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('X', '\\')
|
|
|
84 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
|
|
|
85 #end if
|
|
|
86 #if '__sq__' in str($pdefaultgroupcolumn):
|
|
|
87 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__sq__', "'")
|
|
|
88 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
|
|
|
89 #end if
|
|
|
90 #if '__db__' in str($pdefaultgroupcolumn):
|
|
|
91 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__db__', '"')
|
|
|
92 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
|
|
|
93 #end if
|
|
|
94
|
|
|
95 #if str($pdefaultgroupcolumn):
|
|
|
96 --p-default-group-column=$pdefaultgroupcolumn
|
|
|
97 #end if
|
|
|
98
|
|
|
99 #if str($pyscale) != 'None':
|
|
|
100 --p-yscale=$pyscale
|
|
|
101 #end if
|
|
|
102
|
|
|
103 #if str($pimportancethreshold) != 'None':
|
|
|
104 --p-importance-threshold=$pimportancethreshold
|
|
|
105 #end if
|
|
|
106
|
|
|
107 #if str($pfeaturecount) != 'None':
|
|
|
108 --p-feature-count=$pfeaturecount
|
|
|
109 #end if
|
|
|
110
|
|
|
111 #if str($pmissingsamples) != 'None':
|
|
|
112 --p-missing-samples=$pmissingsamples
|
|
|
113 #end if
|
|
|
114
|
|
|
115 --o-visualization=ovisualization
|
|
|
116
|
|
|
117 #if str($examples) != 'None':
|
|
|
118 --examples=$examples
|
|
|
119 #end if
|
|
|
120
|
|
|
121 ;
|
|
|
122 cp odistancematrix.qza $odistancematrix
|
|
|
123
|
|
|
124 ;
|
|
|
125 qiime tools export ovisualization.qzv --output-path out
|
|
|
126 && mkdir -p '$ovisualization.files_path'
|
|
|
127 && cp -r out/* '$ovisualization.files_path'
|
|
|
128 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
129
|
|
|
130 ;
|
|
|
131 qiime tools export ovisualization.qzv --output-path out
|
|
|
132 && mkdir -p '$ovisualization.files_path'
|
|
|
133 && cp -r out/* '$ovisualization.files_path'
|
|
|
134 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
135
|
|
|
136 ;
|
|
|
137 qiime tools export ovisualization.qzv --output-path out
|
|
|
138 && mkdir -p '$ovisualization.files_path'
|
|
|
139 && cp -r out/* '$ovisualization.files_path'
|
|
|
140 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
141
|
|
|
142 ]]></command>
|
|
|
143 <inputs>
|
|
|
144 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing features found in importances. [required]" name="itable" optional="False" type="data" />
|
|
|
145 <param format="qza,no_unzip.zip" label="--i-importances: ARTIFACT FeatureData[Importance] Feature importance scores. [required]" name="iimportances" optional="False" type="data" />
|
|
|
146 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
|
|
|
147 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata file containing arguments will be individual-id-column. merged) [required]" name="additional_input" optional="False" type="data" />
|
|
|
148 </repeat>
|
|
|
149 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
|
|
|
150 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="False" type="text" />
|
|
|
151 <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="False" type="text" />
|
|
|
152 <param label="--p-yscale: " name="pyscale" optional="True" type="select">
|
|
|
153 <option selected="True" value="None">Selection is Optional</option>
|
|
|
154 <option value="linear">linear</option>
|
|
|
155 <option value="pow">pow</option>
|
|
|
156 <option value="sqrt">sqrt</option>
|
|
|
157 <option value="log">log</option>
|
|
|
158 </param>
|
|
|
159 <param label="--p-importance-threshold: " name="pimportancethreshold" optional="True" type="select">
|
|
|
160 <option selected="True" value="None">Selection is Optional</option>
|
|
|
161 <option value="Float % Range(0">Float % Range(0</option>
|
|
|
162 <option value="None">None</option>
|
|
|
163 <option value="inclusive_start=False">inclusive_start=False</option>
|
|
|
164 </param>
|
|
|
165 <param label="--p-feature-count: " name="pfeaturecount" optional="True" type="select">
|
|
|
166 <option selected="True" value="None">Selection is Optional</option>
|
|
|
167 <option value="Int % Range(1">Int % Range(1</option>
|
|
|
168 <option value="None">None</option>
|
|
|
169 </param>
|
|
|
170 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
|
|
|
171 <option selected="True" value="None">Selection is Optional</option>
|
|
|
172 <option value="error">error</option>
|
|
|
173 <option value="ignore">ignore</option>
|
|
|
174 </param>
|
|
|
175 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
176
|
|
|
177 </inputs>
|
|
|
178
|
|
|
179 <outputs>
|
|
|
180 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
|
|
|
181
|
|
|
182 </outputs>
|
|
|
183
|
|
|
184 <help><![CDATA[
|
|
|
185 Plot longitudinal feature volatility and importances
|
|
|
186 ###############################################################
|
|
|
187
|
|
|
188 Plots an interactive control chart of feature abundances (y-axis) in each
|
|
|
189 sample across time (or state; x-axis). Feature importance scores and
|
|
|
190 descriptive statistics for each feature are plotted in interactive bar
|
|
|
191 charts below the control chart, facilitating exploration of longitudinal
|
|
|
192 feature data. This visualization is intended for use with the feature-
|
|
|
193 volatility pipeline; use that pipeline to access this visualization.
|
|
|
194
|
|
|
195 Parameters
|
|
|
196 ----------
|
|
|
197 table : FeatureTable[RelativeFrequency]
|
|
|
198 Feature table containing features found in importances.
|
|
|
199 importances : FeatureData[Importance]
|
|
|
200 Feature importance scores.
|
|
|
201 metadata : Metadata
|
|
|
202 Sample metadata file containing individual_id_column.
|
|
|
203 state_column : Str
|
|
|
204 Metadata column containing state (time) variable information.
|
|
|
205 individual_id_column : Str, optional
|
|
|
206 Metadata column containing IDs for individual subjects.
|
|
|
207 default_group_column : Str, optional
|
|
|
208 The default metadata column on which to separate groups for comparison
|
|
|
209 (all categorical metadata columns will be available in the
|
|
|
210 visualization).
|
|
|
211 yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
|
|
|
212 y-axis scaling strategy to apply.
|
|
|
213 importance_threshold : Float % Range(0, None, inclusive_start=False) | Str % Choices('q1', 'q2', 'q3'), optional
|
|
|
214 Filter feature table to exclude any features with an importance score
|
|
|
215 less than this threshold. Set to "q1", "q2", or "q3" to select the
|
|
|
216 first, second, or third quartile of values. Set to "None" to disable
|
|
|
217 this filter.
|
|
|
218 feature_count : Int % Range(1, None) | Str % Choices('all'), optional
|
|
|
219 Filter feature table to include top N most important features. Set to
|
|
|
220 "all" to include all features.
|
|
|
221 missing_samples : Str % Choices('error', 'ignore'), optional
|
|
|
222 How to handle missing samples in metadata. "error" will fail if missing
|
|
|
223 samples are detected. "ignore" will cause the feature table and
|
|
|
224 metadata to be filtered, so that only samples found in both files are
|
|
|
225 retained.
|
|
|
226
|
|
|
227 Returns
|
|
|
228 -------
|
|
|
229 visualization : Visualization
|
|
|
230 ]]></help>
|
|
|
231 <macros>
|
|
|
232 <import>qiime_citation.xml</import>
|
|
|
233 </macros>
|
|
|
234 <expand macro="qiime_citation"/>
|
|
|
235 </tool> |
