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comparison qiime2-2020.8/qiime_longitudinal_anova.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_anova" name="qiime longitudinal anova"
3 version="2020.8">
4 <description>ANOVA test</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime longitudinal anova
10 # if $input_files_mmetadatafile:
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 $file_list
17 # end def
18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
19 # end if
20
21 #if $pformula:
22 --p-formula
23 #end if
24
25 #if str($psstype) != 'None':
26 --p-sstype=$psstype
27 #end if
28
29 --o-visualization=ovisualization
30
31 #if str($examples) != 'None':
32 --examples=$examples
33 #end if
34
35 ;
36 cp ohierarchy.qza $ohierarchy
37
38 ;
39 qiime tools export ovisualization.qzv --output-path out
40 && mkdir -p '$ovisualization.files_path'
41 && cp -r out/* '$ovisualization.files_path'
42 && mv '$ovisualization.files_path/index.html' '$ovisualization'
43
44 ]]></command>
45 <inputs>
46 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
47 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata containing formula terms. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
48 </repeat>
49 <param label="--p-formula: --p-formula: TEXT R-style formula specifying the model. All terms must be present in the sample metadata or metadata-transformable artifacts and can be continuous or categorical metadata columns. Formulae will be in the format \'a ~ b + c\', where \'a\' is the metric (dependent variable) and \'b\' and \'c\' are independent covariates. Use \'+\' to add a variable; \'+ a:b\' to add an interaction between variables a and b; \'*\' to include a variable and all interactions; and \'-\' to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" selected="False" type="boolean" />
50 <param label="--p-sstype: " name="psstype" optional="True" type="select">
51 <option selected="True" value="None">Selection is Optional</option>
52 <option value="I">I</option>
53 <option value="II">II</option>
54 <option value="III">III</option>
55 </param>
56 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
57
58 </inputs>
59
60 <outputs>
61 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
62
63 </outputs>
64
65 <help><![CDATA[
66 ANOVA test
67 ###############################################################
68
69 Perform an ANOVA test on any factors present in a metadata file and/or
70 metadata-transformable artifacts. This is followed by pairwise t-tests to
71 examine pairwise differences between categorical sample groups.
72
73 Parameters
74 ----------
75 metadata : Metadata
76 Sample metadata containing formula terms.
77 formula : Str
78 R-style formula specifying the model. All terms must be present in the
79 sample metadata or metadata-transformable artifacts and can be
80 continuous or categorical metadata columns. Formulae will be in the
81 format "a ~ b + c", where "a" is the metric (dependent variable) and
82 "b" and "c" are independent covariates. Use "+" to add a variable; "+
83 a:b" to add an interaction between variables a and b; "*" to include a
84 variable and all interactions; and "-" to subtract a particular term
85 (e.g., an interaction term). See
86 https://patsy.readthedocs.io/en/latest/formulas.html for full
87 documentation of valid formula operators. Always enclose formulae in
88 quotes to avoid unpleasant surprises.
89 sstype : Str % Choices('I', 'II', 'III'), optional
90 Type of sum of squares calculation to perform (I, II, or III).
91
92 Returns
93 -------
94 visualization : Visualization
95 ]]></help>
96 <macros>
97 <import>qiime_citation.xml</import>
98 </macros>
99 <expand macro="qiime_citation"/>
100 </tool>