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comparison qiime2-2020.8/qiime_longitudinal_plot-feature-volatility.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
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>