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comparison qiime2/qiime_longitudinal_volatility.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility"
3 version="2020.8">
4 <description>Generate interactive volatility plot</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime longitudinal volatility
10
11 #if str($itable) != 'None':
12 --i-table=$itable
13 #end if
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=$pdefaultgroupcolumn
97 #end if
98
99 #if str($pdefaultmetric):
100 --p-default-metric=$pdefaultmetric
101 #end if
102 #if str($pyscale) != 'None':
103 --p-yscale=$pyscale
104 #end if
105
106 --o-visualization=ovisualization
107
108 #if str($examples) != 'None':
109 --examples=$examples
110 #end if
111
112 ;
113 cp odistancematrix.qza $odistancematrix
114
115 ;
116 qiime tools export ovisualization.qzv --output-path out
117 && mkdir -p '$ovisualization.files_path'
118 && cp -r out/* '$ovisualization.files_path'
119 && mv '$ovisualization.files_path/index.html' '$ovisualization'
120
121 ;
122 qiime tools export ovisualization.qzv --output-path out
123 && mkdir -p '$ovisualization.files_path'
124 && cp -r out/* '$ovisualization.files_path'
125 && mv '$ovisualization.files_path/index.html' '$ovisualization'
126
127 ;
128 qiime tools export ovisualization.qzv --output-path out
129 && mkdir -p '$ovisualization.files_path'
130 && cp -r out/* '$ovisualization.files_path'
131 && mv '$ovisualization.files_path/index.html' '$ovisualization'
132
133 ;
134 qiime tools export ovisualization.qzv --output-path out
135 && mkdir -p '$ovisualization.files_path'
136 && cp -r out/* '$ovisualization.files_path'
137 && mv '$ovisualization.files_path/index.html' '$ovisualization'
138
139 ]]></command>
140 <inputs>
141 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metrics. [optional]" name="itable" optional="False" type="data" />
142 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
143 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata file containing arguments will be individual-id-column. merged) [required]" name="additional_input" optional="False" type="data" />
144 </repeat>
145 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
146 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="False" type="text" />
147 <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="False" type="text" />
148 <param label="--p-default-metric: TEXT Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization). [optional]" name="pdefaultmetric" optional="False" type="text" />
149 <param label="--p-yscale: " name="pyscale" optional="True" type="select">
150 <option selected="True" value="None">Selection is Optional</option>
151 <option value="linear">linear</option>
152 <option value="pow">pow</option>
153 <option value="sqrt">sqrt</option>
154 <option value="log">log</option>
155 </param>
156 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
157
158 </inputs>
159
160 <outputs>
161 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
162
163 </outputs>
164
165 <help><![CDATA[
166 Generate interactive volatility plot
167 ###############################################################
168
169 Generate an interactive control chart depicting the longitudinal volatility
170 of sample metadata and/or feature frequencies across time (as set using the
171 "state_column" parameter). Any numeric metadata column (and metadata-
172 transformable artifacts, e.g., alpha diversity results) can be plotted on
173 the y-axis, and are selectable using the "metric_column" selector. Metric
174 values are averaged to compare across any categorical metadata column using
175 the "group_column" selector. Longitudinal volatility for individual
176 subjects sampled over time is co-plotted as "spaghetti" plots if the
177 "individual_id_column" parameter is used. state_column will typically be a
178 measure of time, but any numeric metadata column can be used.
179
180 Parameters
181 ----------
182 metadata : Metadata
183 Sample metadata file containing individual_id_column.
184 state_column : Str
185 Metadata column containing state (time) variable information.
186 individual_id_column : Str, optional
187 Metadata column containing IDs for individual subjects.
188 default_group_column : Str, optional
189 The default metadata column on which to separate groups for comparison
190 (all categorical metadata columns will be available in the
191 visualization).
192 default_metric : Str, optional
193 Numeric metadata or artifact column to test by default (all numeric
194 metadata columns will be available in the visualization).
195 table : FeatureTable[RelativeFrequency], optional
196 Feature table containing metrics.
197 yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
198 y-axis scaling strategy to apply.
199
200 Returns
201 -------
202 visualization : Visualization
203 ]]></help>
204 <macros>
205 <import>qiime_citation.xml</import>
206 </macros>
207 <expand macro="qiime_citation"/>
208 </tool>