annotate qiime2/qiime_longitudinal_feature-volatility.xml @ 14:a0a8d77a991c draft

Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
2 <tool id="qiime_longitudinal_feature-volatility" name="qiime longitudinal feature-volatility"
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
3 version="2020.8">
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
4 <description>Feature volatility analysis</description>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
5 <requirements>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
6 <requirement type="package" version="2020.8">qiime2</requirement>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
7 </requirements>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
8 <command><![CDATA[
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9 qiime longitudinal feature-volatility
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-table=$itable
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
12 # if $input_files_mmetadatafile:
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
13 # def list_dict_to_string(list_dict):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
15 # for d in list_dict[1:]:
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
17 # end for
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
18 # return $file_list
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
19 # end def
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
21 # end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
22
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
23 #if '__ob__' in str($pstatecolumn):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
24 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
25 #set $pstatecolumn = $pstatecolumn_temp
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
26 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
27 #if '__cb__' in str($pstatecolumn):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
28 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
29 #set $pstatecolumn = $pstatecolumn_temp
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
30 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
31 #if 'X' in str($pstatecolumn):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
32 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
33 #set $pstatecolumn = $pstatecolumn_temp
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
34 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
35 #if '__sq__' in str($pstatecolumn):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
36 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
37 #set $pstatecolumn = $pstatecolumn_temp
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
38 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
39 #if '__db__' in str($pstatecolumn):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
40 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
41 #set $pstatecolumn = $pstatecolumn_temp
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
42 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
43
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
44 --p-state-column=$pstatecolumn
4
florianbegusch
parents: 0
diff changeset
45
florianbegusch
parents: 0
diff changeset
46
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
47 #if '__ob__' in str($pindividualidcolumn):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
48 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
49 #set $pindividualidcolumn = $pindividualidcolumn_temp
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
50 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
51 #if '__cb__' in str($pindividualidcolumn):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
52 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
53 #set $pindividualidcolumn = $pindividualidcolumn_temp
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
54 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
55 #if 'X' in str($pindividualidcolumn):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
56 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
57 #set $pindividualidcolumn = $pindividualidcolumn_temp
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
58 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
59 #if '__sq__' in str($pindividualidcolumn):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
60 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
61 #set $pindividualidcolumn = $pindividualidcolumn_temp
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
62 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
63 #if '__db__' in str($pindividualidcolumn):
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
64 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
65 #set $pindividualidcolumn = $pindividualidcolumn_temp
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
66 #end if
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 #if str($pindividualidcolumn):
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
69 --p-individual-id-column=$pindividualidcolumn
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
72 --p-cv=$pcv
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 #if str($prandomstate):
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
75 --p-random-state=$prandomstate
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 #end if
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
77 --p-n-jobs=$pnjobs
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
79 --p-n-estimators=$pnestimators
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 #if str($pestimator) != 'None':
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
82 --p-estimator=$pestimator
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 #if $pparametertuning:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 --p-parameter-tuning
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89 #if str($pmissingsamples) != 'None':
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
90 --p-missing-samples=$pmissingsamples
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
91 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
92
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
93 #if str($pimportancethreshold) != 'None':
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
94 --p-importance-threshold=$pimportancethreshold
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
95 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
96
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
97 #if str($pfeaturecount) != 'None':
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
98 --p-feature-count=$pfeaturecount
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
99 #end if
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
100
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
101 --o-filtered-table=ofilteredtable
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
102
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
103 --o-feature-importance=ofeatureimportance
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
104
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
105 --o-volatility-plot=ovolatilityplot
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
106
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
107 --o-accuracy-results=oaccuracyresults
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
108
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
109 --o-sample-estimator=osampleestimator
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
110
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
111 #if str($examples) != 'None':
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
112 --examples=$examples
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
113 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
114
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
115 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
116 cp osampleestimator.qza $osampleestimator
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
117
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
118 ]]></command>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
119 <inputs>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
120 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction. [required]" name="itable" optional="False" type="data" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
121 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
122 <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" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
123 </repeat>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
124 <param label="--p-state-column: TEXT Metadata containing collection time (state) values for each sample. Must contain exclusively numeric values. [required]" name="pstatecolumn" optional="False" type="text" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
125 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="False" type="text" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
126 <param label="--p-cv: INTEGER Number of k-fold cross-validations to perform. Range(1, None) [default: 5]" min="1" name="pcv" optional="True" type="integer" value="5" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
127 <param label="--p-random-state: INTEGER Seed used by random number generator. [optional]" name="prandomstate" optional="False" type="text" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
128 <param label="--p-n-estimators: INTEGER Range(1, None) Number of trees to grow for estimation. More trees will improve predictive accuracy up to a threshold level, but will also increase time and memory requirements. This parameter only affects ensemble estimators, such as Random Forest, AdaBoost, ExtraTrees, and GradientBoosting. [default: 100]" min="1" name="pnestimators" optional="True" type="integer" value="100" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
129 <param label="--p-estimator: " name="pestimator" optional="True" type="select">
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
130 <option selected="True" value="None">Selection is Optional</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
131 <option value="RandomForestRegressor">RandomForestRegressor</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
132 <option value="ExtraTreesRegressor">ExtraTreesRegressor</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
133 <option value="GradientBoostingRegressor">GradientBoostingRegressor</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
134 <option value="AdaBoostRegressor">AdaBoostRegressor</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
135 <option value="ElasticNet">ElasticNet</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
136 <option value="Ridge">Ridge</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
137 <option value="Lasso">Lasso</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
138 <option value="KNeighborsRegressor">KNeighborsRegressor</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
139 <option value="LinearSVR">LinearSVR</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
140 <option value="SVR">SVR</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
141 </param>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
142 <param label="--p-parameter-tuning: --p-parameter-tuning: / --p-no-parameter-tuning Automatically tune hyperparameters using random grid search. [default: False]" name="pparametertuning" selected="False" type="boolean" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
143 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
144 <option selected="True" value="None">Selection is Optional</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
145 <option value="error">error</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
146 <option value="ignore">ignore</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
147 </param>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
148 <param label="--p-importance-threshold: " name="pimportancethreshold" optional="True" type="select">
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
149 <option selected="True" value="None">Selection is Optional</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
150 <option value="Float % Range(0">Float % Range(0</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
151 <option value="None">None</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
152 <option value="inclusive_start=False">inclusive_start=False</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
153 </param>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
154 <param label="--p-feature-count: " name="pfeaturecount" optional="True" type="select">
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
155 <option selected="True" value="None">Selection is Optional</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
156 <option value="Int % Range(1">Int % Range(1</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
157 <option value="None">None</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
158 </param>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
159 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
160
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
161 </inputs>
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
162
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
163 <outputs>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
164 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
165 <data format="qza" label="${tool.name} on ${on_string}: featureimportance.qza" name="ofeatureimportance" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
166 <data format="html" label="${tool.name} on ${on_string}: volatilityplot.html" name="ovolatilityplot" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
167 <data format="html" label="${tool.name} on ${on_string}: accuracyresults.html" name="oaccuracyresults" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
168 <data format="qza" label="${tool.name} on ${on_string}: sampleestimator.qza" name="osampleestimator" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
169
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
170 </outputs>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
171
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
172 <help><![CDATA[
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
173 Feature volatility analysis
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
174 ###############################################################
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
175
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
176 Identify features that are predictive of a numeric metadata column,
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
177 state_column (e.g., time), and plot their relative frequencies across
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
178 states using interactive feature volatility plots. A supervised learning
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
179 regressor is used to identify important features and assess their ability
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
180 to predict sample states. state_column will typically be a measure of time,
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
181 but any numeric metadata column can be used.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
182
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
183 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
184 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
185 table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
186 Feature table containing all features that should be used for target
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
187 prediction.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
188 metadata : Metadata
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
189 Sample metadata file containing individual_id_column.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
190 state_column : Str
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
191 Metadata containing collection time (state) values for each sample.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
192 Must contain exclusively numeric values.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
193 individual_id_column : Str, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
194 Metadata column containing IDs for individual subjects.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
195 cv : Int % Range(1, None), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
196 Number of k-fold cross-validations to perform.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
197 random_state : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
198 Seed used by random number generator.
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
199 n_jobs : Int, optional
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
200 Number of jobs to run in parallel.
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
201 n_estimators : Int % Range(1, None), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
202 Number of trees to grow for estimation. More trees will improve
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
203 predictive accuracy up to a threshold level, but will also increase
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
204 time and memory requirements. This parameter only affects ensemble
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
205 estimators, such as Random Forest, AdaBoost, ExtraTrees, and
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
206 GradientBoosting.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
207 estimator : Str % Choices('RandomForestRegressor', 'ExtraTreesRegressor', 'GradientBoostingRegressor', 'AdaBoostRegressor', 'ElasticNet', 'Ridge', 'Lasso', 'KNeighborsRegressor', 'LinearSVR', 'SVR'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
208 Estimator method to use for sample prediction.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
209 parameter_tuning : Bool, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
210 Automatically tune hyperparameters using random grid search.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
211 missing_samples : Str % Choices('error', 'ignore'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
212 How to handle missing samples in metadata. "error" will fail if missing
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
213 samples are detected. "ignore" will cause the feature table and
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
214 metadata to be filtered, so that only samples found in both files are
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
215 retained.
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
216 importance_threshold : Float % Range(0, None, inclusive_start=False) | Str % Choices('q1', 'q2', 'q3'), optional
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
217 Filter feature table to exclude any features with an importance score
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
218 less than this threshold. Set to "q1", "q2", or "q3" to select the
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
219 first, second, or third quartile of values. Set to "None" to disable
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
220 this filter.
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
221 feature_count : Int % Range(1, None) | Str % Choices('all'), optional
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
222 Filter feature table to include top N most important features. Set to
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
223 "all" to include all features.
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
224
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
225 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
226 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
227 filtered_table : FeatureTable[RelativeFrequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
228 Feature table containing only important features.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
229 feature_importance : FeatureData[Importance]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
230 Importance of each input feature to model accuracy.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
231 volatility_plot : Visualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
232 Interactive volatility plot visualization.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
233 accuracy_results : Visualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
234 Accuracy results visualization.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
235 sample_estimator : SampleEstimator[Regressor]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
236 Trained sample regressor.
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
237 ]]></help>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
238 <macros>
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
239 <import>qiime_citation.xml</import>
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
240 </macros>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
241 <expand macro="qiime_citation"/>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
242 </tool>