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comparison qiime2/qiime_longitudinal_volatility.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility" version="2019.4">
3 <description> - Generate interactive volatility plot</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime longitudinal volatility
9
10 --p-state-column="$pstatecolumn"
11
12 #if str($itable) != 'None':
13 --i-table=$itable
14 #end if
15
16 #if str($pindividualidcolumn):
17 --p-individual-id-column="$pindividualidcolumn"
18 #end if
19
20 #if str($pdefaultgroupcolumn):
21 --p-default-group-column="$pdefaultgroupcolumn"
22 #end if
23
24 #if str($pdefaultmetric):
25 --p-default-metric="$pdefaultmetric"
26 #end if
27
28 #if str($pyscale) != 'None':
29 --p-yscale=$pyscale
30 #end if
31
32
33 #if $input_files_mmetadatafile:
34 #def list_dict_to_string(list_dict):
35 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
36 #for d in list_dict[1:]:
37 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
38 #end for
39 #return $file_list
40 #end def
41 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
42 #end if
43
44
45 --o-visualization=ovisualization
46 ;
47 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
48 && cp -r out/* '$ovisualization.files_path'
49 && mv '$ovisualization.files_path/index.html' '$ovisualization';
50 ]]></command>
51 <inputs>
52 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/>
53 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metrics. [optional]" name="itable" optional="True" type="data"/>
54 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="True" type="text"/>
55 <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="True" type="text"/>
56 <param label="--p-default-metric: TEXT Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization). [optional]" name="pdefaultmetric" optional="True" type="text"/>
57 <param label="--p-yscale: " name="pyscale" optional="True" type="select">
58 <option selected="True" value="None">Selection is Optional</option>
59 <option value="linear">linear</option>
60 <option value="pow">pow</option>
61 <option value="sqrt">sqrt</option>
62 <option value="log">log</option>
63 </param>
64
65 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
66 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
67 </repeat>
68
69 </inputs>
70 <outputs>
71 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
72 </outputs>
73 <help><![CDATA[
74 Generate interactive volatility plot
75 ####################################
76
77 Generate an interactive control chart depicting the longitudinal volatility
78 of sample metadata and/or feature frequencies across time (as set using the
79 "state_column" parameter). Any numeric metadata column (and metadata-
80 transformable artifacts, e.g., alpha diversity results) can be plotted on
81 the y-axis, and are selectable using the "metric_column" selector. Metric
82 values are averaged to compare across any categorical metadata column using
83 the "group_column" selector. Longitudinal volatility for individual
84 subjects sampled over time is co-plotted as "spaghetti" plots if the
85 "individual_id_column" parameter is used. state_column will typically be a
86 measure of time, but any numeric metadata column can be used.
87
88 Parameters
89 ----------
90 metadata : Metadata
91 Sample metadata file containing individual_id_column.
92 state_column : Str
93 Metadata column containing state (time) variable information.
94 individual_id_column : Str, optional
95 Metadata column containing IDs for individual subjects.
96 default_group_column : Str, optional
97 The default metadata column on which to separate groups for comparison
98 (all categorical metadata columns will be available in the
99 visualization).
100 default_metric : Str, optional
101 Numeric metadata or artifact column to test by default (all numeric
102 metadata columns will be available in the visualization).
103 table : FeatureTable[RelativeFrequency], optional
104 Feature table containing metrics.
105 yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
106 y-axis scaling strategy to apply.
107
108 Returns
109 -------
110 visualization : Visualization
111 ]]></help>
112 <macros>
113 <import>qiime_citation.xml</import>
114 </macros>
115 <expand macro="qiime_citation"/>
116 </tool>