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comparison qiime2/qiime_gneiss_lme-regression.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_gneiss_lme-regression" name="qiime gneiss lme-regression" version="2019.4">
3 <description> - Simplicial Linear mixed effects regression</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime gneiss lme-regression
9
10 --i-table=$itable
11 --i-tree=$itree
12 --p-formula="$pformula"
13 --p-groups="$pgroups"
14
15
16 #if $input_files_mmetadatafile:
17 #def list_dict_to_string(list_dict):
18 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
19 #for d in list_dict[1:]:
20 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
21 #end for
22 #return $file_list
23 #end def
24 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
25 #end if
26
27
28 --o-visualization=ovisualization
29 ;
30 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
31 && cp -r out/* '$ovisualization.files_path'
32 && mv '$ovisualization.files_path/index.html' '$ovisualization';
33 ]]></command>
34 <inputs>
35 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Balance] The feature table containing the samples in which simplicial regression with mixed effect will be performed. [required]" name="itable" optional="False" type="data"/>
36 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT A hierarchy of feature identifiers where each tip Hierarchy corresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="itree" optional="False" type="data"/>
37 <param label="--p-formula: TEXT Statistical formula specifying the statistical model. In other words, a list of the metadata categories that will be used in the linear mixed effect model, typically separated by '+'. For more information see https://patsy.readthedocs.io/en/latest/API-reference.ht ml [required]" name="pformula" optional="False" type="text"/>
38 <param label="--p-groups: TEXT [required]" name="pgroups" optional="False" type="text"/>
39 </inputs>
40 <outputs>
41 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
42 </outputs>
43 <help><![CDATA[
44 Simplicial Linear mixed effects regression
45 ##########################################
46
47 Build and run linear mixed effects model on balances. Use LME over OLS when
48 you have repeated measurements such as (timeseries).
49
50 Parameters
51 ----------
52 table : FeatureTable[Balance]
53 The feature table containing the samples in which simplicial regression
54 with mixed effect will be performed.
55 tree : Hierarchy
56 A hierarchy of feature identifiers where each tip corresponds to the
57 feature identifiers in the table. This tree can contain tip ids that
58 are not present in the table, but all feature ids in the table must be
59 present in this tree.
60 metadata : Metadata
61 Metadata information that contains the covariates of interest.
62 formula : Str
63 Statistical formula specifying the statistical model. In other words, a
64 list of the metadata categories that will be used in the linear mixed
65 effect model, typically separated by "+". For more information see
66 https://patsy.readthedocs.io/en/latest/API-reference.html
67 groups : Str
68 \
69
70 Returns
71 -------
72 visualization : Visualization
73 ]]></help>
74 <macros>
75 <import>qiime_citation.xml</import>
76 </macros>
77 <expand macro="qiime_citation"/>
78 </tool>