|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Nonparametric microbial interdependence test</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime longitudinal nmit
|
|
|
10
|
|
|
11 --i-table=$itable
|
|
|
12 # if $input_files_mmetadatafile:
|
|
|
13 # def list_dict_to_string(list_dict):
|
|
|
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
15 # for d in list_dict[1:]:
|
|
|
16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
|
17 # end for
|
|
|
18 # return $file_list
|
|
|
19 # end def
|
|
|
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
|
21 # end if
|
|
|
22
|
|
|
23 #if '__ob__' in str($pindividualidcolumn):
|
|
|
24 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
|
|
|
25 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
26 #end if
|
|
|
27 #if '__cb__' in str($pindividualidcolumn):
|
|
|
28 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
|
|
|
29 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
30 #end if
|
|
|
31 #if 'X' in str($pindividualidcolumn):
|
|
|
32 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
|
|
|
33 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
34 #end if
|
|
|
35 #if '__sq__' in str($pindividualidcolumn):
|
|
|
36 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
|
|
|
37 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
38 #end if
|
|
|
39 #if '__db__' in str($pindividualidcolumn):
|
|
|
40 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
|
|
|
41 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
42 #end if
|
|
|
43
|
|
|
44 --p-individual-id-column=$pindividualidcolumn
|
|
|
45
|
|
|
46
|
|
|
47 #if str($pcorrmethod) != 'None':
|
|
|
48 --p-corr-method=$pcorrmethod
|
|
|
49 #end if
|
|
|
50
|
|
|
51 #if str($pdistmethod) != 'None':
|
|
|
52 --p-dist-method=$pdistmethod
|
|
|
53 #end if
|
|
|
54
|
|
|
55 --o-distance-matrix=odistancematrix
|
|
|
56
|
|
|
57 #if str($examples) != 'None':
|
|
|
58 --examples=$examples
|
|
|
59 #end if
|
|
|
60
|
|
|
61 ;
|
|
|
62 cp odistancematrix.qza $odistancematrix
|
|
|
63
|
|
|
64 ]]></command>
|
|
|
65 <inputs>
|
|
|
66 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test. [required]" name="itable" optional="False" type="data" />
|
|
|
67 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
|
|
|
68 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata file containing individual-id-column. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
|
|
|
69 </repeat>
|
|
|
70 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text" />
|
|
|
71 <param label="--p-corr-method: " name="pcorrmethod" optional="True" type="select">
|
|
|
72 <option selected="True" value="None">Selection is Optional</option>
|
|
|
73 <option value="kendall">kendall</option>
|
|
|
74 <option value="pearson">pearson</option>
|
|
|
75 <option value="spearman">spearman</option>
|
|
|
76 </param>
|
|
|
77 <param label="--p-dist-method: " name="pdistmethod" optional="True" type="select">
|
|
|
78 <option selected="True" value="None">Selection is Optional</option>
|
|
|
79 <option value="fro">fro</option>
|
|
|
80 <option value="nuc">nuc</option>
|
|
|
81 </param>
|
|
|
82 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
83
|
|
|
84 </inputs>
|
|
|
85
|
|
|
86 <outputs>
|
|
|
87 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
|
|
|
88
|
|
|
89 </outputs>
|
|
|
90
|
|
|
91 <help><![CDATA[
|
|
|
92 Nonparametric microbial interdependence test
|
|
|
93 ###############################################################
|
|
|
94
|
|
|
95 Perform nonparametric microbial interdependence test to determine
|
|
|
96 longitudinal sample similarity as a function of temporal microbial
|
|
|
97 composition. For more details and citation, please see
|
|
|
98 doi.org/10.1002/gepi.22065
|
|
|
99
|
|
|
100 Parameters
|
|
|
101 ----------
|
|
|
102 table : FeatureTable[RelativeFrequency]
|
|
|
103 Feature table to use for microbial interdependence test.
|
|
|
104 metadata : Metadata
|
|
|
105 Sample metadata file containing individual_id_column.
|
|
|
106 individual_id_column : Str
|
|
|
107 Metadata column containing IDs for individual subjects.
|
|
|
108 corr_method : Str % Choices('kendall', 'pearson', 'spearman'), optional
|
|
|
109 The temporal correlation test to be applied.
|
|
|
110 dist_method : Str % Choices('fro', 'nuc'), optional
|
|
|
111 Temporal distance method, see numpy.linalg.norm for details.
|
|
|
112
|
|
|
113 Returns
|
|
|
114 -------
|
|
|
115 distance_matrix : DistanceMatrix
|
|
|
116 The resulting distance matrix.
|
|
|
117 ]]></help>
|
|
|
118 <macros>
|
|
|
119 <import>qiime_citation.xml</import>
|
|
|
120 </macros>
|
|
|
121 <expand macro="qiime_citation"/>
|
|
|
122 </tool> |
