|
0
|
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>
|
