Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/qiime_longitudinal_nmit.xml @ 29:3ba9833030c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
parents
children
comparison
equal deleted inserted replaced
28:c28331a63dfd 29:3ba9833030c1
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>