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comparison qiime_gneiss_lme-regression.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_lme-regression" name="qiime gneiss lme-regression" version="2018.4">
3 <description> - Simplicial Linear mixed effects regression</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime gneiss lme-regression --i-table=$itable
10
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 + ',' + d['additional_input'].__getattr__('file_name')
15 #end for
16 #return $file_list
17 #end def
18
19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --i-tree=$itree --p-groups="$pgroups" --p-formula="$pformula"
20 #if str($cmdconfig) != 'None':
21 --cmd-config=$cmdconfig
22 #end if
23 --o-visualization=ovisualization;
24
25 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
26 && cp -r out/* '$ovisualization.files_path'
27 && mv '$ovisualization.files_path/index.html' '$ovisualization'
28 ]]>
29 </command>
30 <inputs>
31 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Balance] The feature table containing the samples in which simplicial regression with mixed effects will be performedwill be performed. [required]" name="itable" optional="False" type="data"/>
32 <param format="qza,no_unzip.zip" label="--i-tree: Hierarchy A hierarchy of feature identifiers where each 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"/>
33 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
34 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Metadata information that contains the covariates of interest. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
35 </repeat>
36
37 <param label="--p-formula: Statistical formula specifying the statistical model. [required]" name="pformula" optional="False" type="text"/>
38 <param label="--p-groups: [required]" name="pgroups" optional="False" type="text"/>
39
40 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
41 </inputs>
42 <outputs>
43 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
44 </outputs>
45 <help>
46 <![CDATA[
47 Simplicial Linear mixed effects regression
48 -------------------------------------------
49
50 Build and run linear mixed effects model on balances.
51
52 Parameters
53 ----------
54 table : FeatureTable[Balance]
55 The feature table containing the samples in which simplicial regression
56 with mixed effects will be performedwill be performed.
57 tree : Hierarchy
58 A hierarchy of feature identifiers where each tipcorresponds to the
59 feature identifiers in the table. This tree can contain tip ids that
60 are not present in the table, but all feature ids in the table must be
61 present in this tree.
62 metadata : Metadata
63 Metadata information that contains the covariates of interest.
64 formula : Str
65 Statistical formula specifying the statistical model.
66 groups : Str
67 \
68
69 Returns
70 -------
71 visualization : Visualization
72 \
73 ]]>
74 </help>
75 </tool>