Mercurial > repos > florianbegusch > qiime2_suite_zmf
comparison qiime2-2020.8/qiime_longitudinal_anova.xml @ 0:5c352d975ef7 draft
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author | florianbegusch |
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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> |