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comparison qiime2/qiime_longitudinal_volatility.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility" version="2018.4">
3 <description> - Volatility analysis</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime longitudinal volatility --p-state-column="$pstatecolumn"
10
11 #def list_dict_to_string(list_dict):
12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 #for d in list_dict[1:]:
14 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
15 #end for
16 #return $file_list
17 #end def
18
19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
20 --p-default-group-column="$pdefaultgroupcolumn"
21 --p-individual-id-column="$pindividualidcolumn"
22 --p-default-metric="$pdefaultmetric"
23 #if str($itable) != 'None':
24 --i-table=$itable
25 #end if
26
27 #if str($cmdconfig) != 'None':
28 --cmd-config=$cmdconfig
29 #end if
30 --o-visualization=ovisualization
31
32 #if str($pyscale) != 'None':
33 --p-yscale=$pyscale
34 #end if
35 ;
36 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
37 && cp -r out/* '$ovisualization.files_path'
38 && mv '$ovisualization.files_path/index.html' '$ovisualization'
39 ]]>
40 </command>
41 <inputs>
42 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
43 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
44 </repeat>
45
46 <param label="--p-state-column: Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/>
47
48 <param label="--p-individual-id-column: Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
49
50 <param label="--p-default-group-column: The default metadata column on which to
51 separate groups for comparison (all
52 categorical metadata columns will be
53 available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="False" type="text"/>
54
55 <param label="--p-default-metric: Numeric metadata or artifact column to test
56 by default (all numeric metadata columns
57 will be available in the visualization).
58 [optional]" name="pdefaultmetric" optional="False" type="text"/>
59
60 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[RelativeFrequency] Feature table to optionally use for paired comparisons. [optional]" name="itable" optional="True" type="data"/>
61
62 <param label="--p-yscale: y-axis scaling strategy to apply. [default:
63 linear]" name="pyscale" optional="True" type="select">
64 <option selected="True" value="None">Selection is Optional</option>
65 <option value="pow">log</option>
66 <option value="linear">logit</option>
67 <option value="sqrt">symlog</option>
68 <option value="log">linear</option>
69 </param>
70
71 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
72 </inputs>
73 <outputs>
74 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
75 </outputs>
76 <help>
77 <![CDATA[
78 Volatility analysis
79 --------------------
80
81 Plot an interactive control chart of a single dependent variable, "metric",
82 across multiple groups contained in sample metadata column "group_column".
83
84 Parameters
85 ----------
86 table : FeatureTable[RelativeFrequency], optional
87 Feature table to optionally use for paired comparisons.
88 metadata : Metadata
89 Sample metadata file containing individual_id_column.
90 state_column : Str
91 Metadata column containing state (e.g., Time) across which samples are
92 paired.
93 individual_id_column : Str
94 Metadata column containing IDs for individual subjects.
95 default_group_column : Str, optional
96 The default metadata column on which to separate groups for comparison
97 (all categorical metadata columns will be available in the
98 visualization).
99 default_metric : Str, optional
100 Numeric metadata or artifact column to test by default (all numeric
101 metadata columns will be available in the visualization).
102 yscale : Str % Choices({'linear', 'log', 'pow', 'sqrt'}), optional
103 y-axis scaling strategy to apply.
104
105 Returns
106 -------
107 visualization : Visualization
108 \
109 ]]>
110 </help>
111 <macros>
112 <import>qiime_citation.xml</import>
113 </macros>
114 <expand macro="qiime_citation" />
115 </tool>