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