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comparison qiime2/qiime_longitudinal_nmit.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_longitudinal_nmit" name="qiime longitudinal nmit" version="2019.4">
3 <description> - Nonparametric microbial interdependence test</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime longitudinal nmit
9
10 --i-table=$itable
11 --p-individual-id-column="$pindividualidcolumn"
12
13 #if str($pcorrmethod) != 'None':
14 --p-corr-method=$pcorrmethod
15 #end if
16
17 #if str($pdistmethod) != 'None':
18 --p-dist-method=$pdistmethod
19 #end if
20
21
22 #if $input_files_mmetadatafile:
23 #def list_dict_to_string(list_dict):
24 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
25 #for d in list_dict[1:]:
26 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
27 #end for
28 #return $file_list
29 #end def
30 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
31 #end if
32
33
34 --o-distance-matrix=odistancematrix
35 ;
36 cp odistancematrix.qza $odistancematrix
37 ]]></command>
38 <inputs>
39 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test. [required]" name="itable" optional="False" type="data"/>
40 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
41 <param label="--p-corr-method: " name="pcorrmethod" optional="True" type="select">
42 <option selected="True" value="None">Selection is Optional</option>
43 <option value="kendall">kendall</option>
44 <option value="pearson">pearson</option>
45 <option value="spearman">spearman</option>
46 </param>
47 <param label="--p-dist-method: " name="pdistmethod" optional="True" type="select">
48 <option selected="True" value="None">Selection is Optional</option>
49 <option value="fro">fro</option>
50 <option value="nuc">nuc</option>
51 </param>
52
53 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
54 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
55 </repeat>
56
57 </inputs>
58 <outputs>
59 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/>
60 </outputs>
61 <help><![CDATA[
62 Nonparametric microbial interdependence test
63 ############################################
64
65 Perform nonparametric microbial interdependence test to determine
66 longitudinal sample similarity as a function of temporal microbial
67 composition. For more details and citation, please see
68 doi.org/10.1002/gepi.22065
69
70 Parameters
71 ----------
72 table : FeatureTable[RelativeFrequency]
73 Feature table to use for microbial interdependence test.
74 metadata : Metadata
75 Sample metadata file containing individual_id_column.
76 individual_id_column : Str
77 Metadata column containing IDs for individual subjects.
78 corr_method : Str % Choices('kendall', 'pearson', 'spearman'), optional
79 The temporal correlation test to be applied.
80 dist_method : Str % Choices('fro', 'nuc'), optional
81 Temporal distance method, see numpy.linalg.norm for details.
82
83 Returns
84 -------
85 distance_matrix : DistanceMatrix
86 The resulting distance matrix.
87 ]]></help>
88 <macros>
89 <import>qiime_citation.xml</import>
90 </macros>
91 <expand macro="qiime_citation"/>
92 </tool>