|
0
|
1 <?xml version="1.0" ?>
|
|
9
|
2 <tool id="qiime_longitudinal_anova" name="qiime longitudinal anova" version="2019.7">
|
|
0
|
3 <description> - ANOVA test</description>
|
|
|
4 <requirements>
|
|
9
|
5 <requirement type="package" version="2019.7">qiime2</requirement>
|
|
0
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime longitudinal anova
|
|
|
9
|
|
4
|
10
|
|
|
11
|
|
|
12
|
|
|
13 #if 'X' in str($pformula):
|
|
|
14 #set $pformula_temp = $pformula.replace('X', "~")
|
|
|
15 #set $pformula = $pformula_temp
|
|
|
16 #end if
|
|
|
17
|
|
0
|
18 --p-formula="$pformula"
|
|
|
19
|
|
4
|
20
|
|
|
21
|
|
0
|
22 #if str($psstype) != 'None':
|
|
|
23 --p-sstype=$psstype
|
|
|
24 #end if
|
|
|
25
|
|
|
26
|
|
|
27 #if $input_files_mmetadatafile:
|
|
|
28 #def list_dict_to_string(list_dict):
|
|
|
29 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
30 #for d in list_dict[1:]:
|
|
|
31 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
|
32 #end for
|
|
|
33 #return $file_list
|
|
|
34 #end def
|
|
|
35 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
|
36 #end if
|
|
|
37
|
|
|
38
|
|
|
39 --o-visualization=ovisualization
|
|
|
40 ;
|
|
|
41 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
42 && cp -r out/* '$ovisualization.files_path'
|
|
|
43 && mv '$ovisualization.files_path/index.html' '$ovisualization';
|
|
|
44 ]]></command>
|
|
|
45 <inputs>
|
|
|
46 <param label="--p-formula: TEXT R-style formula specifying the model. All terms must be present in the sample metadata or metadata-transformable artifacts and can be continuous or categorical metadata columns. Formulae will be in the format 'a ~ b + c', where 'a' is the metric (dependent variable) and 'b' and 'c' are independent covariates. Use '+' to add a variable; '+ a:b' to add an interaction between variables a and b; '*' to include a variable and all interactions; and '-' to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" optional="False" type="text"/>
|
|
|
47 <param label="--p-sstype: " name="psstype" optional="True" type="select">
|
|
|
48 <option selected="True" value="None">Selection is Optional</option>
|
|
|
49 <option value="I">I</option>
|
|
|
50 <option value="II">II</option>
|
|
|
51 <option value="III">III</option>
|
|
|
52 </param>
|
|
|
53
|
|
|
54 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
|
|
|
55 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
|
56 </repeat>
|
|
|
57
|
|
|
58 </inputs>
|
|
|
59 <outputs>
|
|
|
60 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
61 </outputs>
|
|
|
62 <help><![CDATA[
|
|
|
63 ANOVA test
|
|
|
64 ##########
|
|
|
65
|
|
|
66 Perform an ANOVA test on any factors present in a metadata file and/or
|
|
|
67 metadata-transformable artifacts. This is followed by pairwise t-tests to
|
|
|
68 examine pairwise differences between categorical sample groups.
|
|
|
69
|
|
|
70 Parameters
|
|
|
71 ----------
|
|
|
72 metadata : Metadata
|
|
|
73 Sample metadata containing formula terms.
|
|
|
74 formula : Str
|
|
|
75 R-style formula specifying the model. All terms must be present in the
|
|
|
76 sample metadata or metadata-transformable artifacts and can be
|
|
|
77 continuous or categorical metadata columns. Formulae will be in the
|
|
|
78 format "a ~ b + c", where "a" is the metric (dependent variable) and
|
|
|
79 "b" and "c" are independent covariates. Use "+" to add a variable; "+
|
|
|
80 a:b" to add an interaction between variables a and b; "*" to include a
|
|
|
81 variable and all interactions; and "-" to subtract a particular term
|
|
|
82 (e.g., an interaction term). See
|
|
|
83 https://patsy.readthedocs.io/en/latest/formulas.html for full
|
|
|
84 documentation of valid formula operators. Always enclose formulae in
|
|
|
85 quotes to avoid unpleasant surprises.
|
|
|
86 sstype : Str % Choices('I', 'II', 'III'), optional
|
|
|
87 Type of sum of squares calculation to perform (I, II, or III).
|
|
|
88
|
|
|
89 Returns
|
|
|
90 -------
|
|
|
91 visualization : Visualization
|
|
|
92 ]]></help>
|
|
|
93 <macros>
|
|
|
94 <import>qiime_citation.xml</import>
|
|
|
95 </macros>
|
|
|
96 <expand macro="qiime_citation"/>
|
|
|
97 </tool>
|
