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

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_anova" name="qiime longitudinal anova" version="2019.4">
3 <description> - ANOVA test</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime longitudinal anova
9
10 --p-formula="$pformula"
11
12 #if str($psstype) != 'None':
13 --p-sstype=$psstype
14 #end if
15
16
17 #if $input_files_mmetadatafile:
18 #def list_dict_to_string(list_dict):
19 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
20 #for d in list_dict[1:]:
21 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
22 #end for
23 #return $file_list
24 #end def
25 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
26 #end if
27
28
29 --o-visualization=ovisualization
30 ;
31 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
32 && cp -r out/* '$ovisualization.files_path'
33 && mv '$ovisualization.files_path/index.html' '$ovisualization';
34 ]]></command>
35 <inputs>
36 <param label="--p-formula: TEXT R-style formula specifying the model. All terms must be present in the sample metadata or metadata-transformable artifacts and can be continuous or categorical metadata columns. Formulae will be in the format 'a ~ b + c', where 'a' is the metric (dependent variable) and 'b' and 'c' are independent covariates. Use '+' to add a variable; '+ a:b' to add an interaction between variables a and b; '*' to include a variable and all interactions; and '-' to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" optional="False" type="text"/>
37 <param label="--p-sstype: " name="psstype" optional="True" type="select">
38 <option selected="True" value="None">Selection is Optional</option>
39 <option value="I">I</option>
40 <option value="II">II</option>
41 <option value="III">III</option>
42 </param>
43
44 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
45 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
46 </repeat>
47
48 </inputs>
49 <outputs>
50 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
51 </outputs>
52 <help><![CDATA[
53 ANOVA test
54 ##########
55
56 Perform an ANOVA test on any factors present in a metadata file and/or
57 metadata-transformable artifacts. This is followed by pairwise t-tests to
58 examine pairwise differences between categorical sample groups.
59
60 Parameters
61 ----------
62 metadata : Metadata
63 Sample metadata containing formula terms.
64 formula : Str
65 R-style formula specifying the model. All terms must be present in the
66 sample metadata or metadata-transformable artifacts and can be
67 continuous or categorical metadata columns. Formulae will be in the
68 format "a ~ b + c", where "a" is the metric (dependent variable) and
69 "b" and "c" are independent covariates. Use "+" to add a variable; "+
70 a:b" to add an interaction between variables a and b; "*" to include a
71 variable and all interactions; and "-" to subtract a particular term
72 (e.g., an interaction term). See
73 https://patsy.readthedocs.io/en/latest/formulas.html for full
74 documentation of valid formula operators. Always enclose formulae in
75 quotes to avoid unpleasant surprises.
76 sstype : Str % Choices('I', 'II', 'III'), optional
77 Type of sum of squares calculation to perform (I, II, or III).
78
79 Returns
80 -------
81 visualization : Visualization
82 ]]></help>
83 <macros>
84 <import>qiime_citation.xml</import>
85 </macros>
86 <expand macro="qiime_citation"/>
87 </tool>