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comparison qiime_gneiss_ols-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_ols-regression" name="qiime gneiss ols-regression" version="2018.4">
3 <description>- Simplicial Ordinary Least Squares Regression</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime gneiss ols-regression
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($input_files_mmetadatafile) --i-table=$itable
20
21 #if '__ob__' in str($pformula):
22 #set $pformula_temp = $pformula.replace('__dp__', '"')
23 #set $pformula = $pformula_temp
24 #end if
25 --p-formula="$pformula"
26
27 --i-tree=$itree
28 #if str($cmdconfig) != 'None':
29 --cmd-config=$cmdconfig
30 #end if
31 --o-visualization=ovisualization;
32
33 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
34 && cp -r out/* '$ovisualization.files_path'
35 && mv '$ovisualization.files_path/index.html' '$ovisualization'
36 ]]>
37 </command>
38 <inputs>
39 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Balance] The feature table containing the samples in which simplicial regression will be performed. [required]" name="itable" optional="False" type="data"/>
40
41 <param format="qza,no_unzip.zip" label="--i-tree: Hierarchy A hierarchy of feature identifiers where each tipcorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="itree" optional="False" type="data"/>
42
43 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
44 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Metadata information that contains the covariates of interest. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
45 </repeat> <param label="--p-formula: Statistical formula specifying the statistical model. [required]" name="pformula" optional="False" type="text"/>
46
47 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
48 </inputs>
49 <outputs>
50 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
51 </outputs>
52 <help><![CDATA[
53 Simplicial Ordinary Least Squares Regression
54 ---------------------------------------------
55
56 Perform linear regression on balances.
57
58 Parameters
59 ----------
60 table : FeatureTable[Balance]
61 The feature table containing the samples in which simplicial regression
62 will be performed.
63 tree : Hierarchy
64 A hierarchy of feature identifiers where each tipcorresponds to the
65 feature identifiers in the table. This tree can contain tip ids that
66 are not present in the table, but all feature ids in the table must be
67 present in this tree.
68 metadata : Metadata
69 Metadata information that contains the covariates of interest.
70 formula : Str
71 Statistical formula specifying the statistical model.
72
73 Returns
74 -------
75 visualization : Visualization
76 \
77 ]]>
78 </help>
79 </tool>