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comparison qiime2/qiime_longitudinal_nmit.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit" version="2018.4">
3 <description> - Nonparametric microbial interdependence test</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime longitudinal nmit --i-table=$itable
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($input_files_mmetadatafile) --p-individual-id-column="$pindividualidcolumn"
20 #if str($cmdconfig) != 'None':
21 --cmd-config=$cmdconfig
22 #end if
23
24 #if str($pdistmethod) != 'None':
25 --p-dist-method=$pdistmethod
26 #end if
27
28 #if str($pcorrmethod) != 'None':
29 --p-corr-method=$pcorrmethod
30 #end if
31 --o-distance-matrix=odistancematrix;
32
33 cp odistancematrix.qza $odistancematrix;
34 ]]>
35 </command>
36 <inputs>
37 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test. [required]" name="itable" optional="False" type="data"/>
38
39 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
40 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
41 </repeat>
42
43 <param label="--p-individual-id-column: Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
44
45 <param label="--p-corr-method: The temporal correlation test to be applied.
46 [default: kendall]" name="pcorrmethod" optional="True" type="select">
47 <option selected="True" value="None">Selection is Optional</option>
48 <option value="kendall">kendall</option>
49 <option value="pearson">pearson</option>
50 <option value="spearman">spearman</option>
51 </param>
52
53 <param label="--p-dist-method: Temporal distance method, see
54 numpy.linalg.norm for details. [default:
55 fro]" name="pdistmethod" optional="True" type="select">
56 <option selected="True" value="None">Selection is Optional</option>
57 <option value="fro">fro</option>
58 <option value="nuc">nuc</option>
59 </param>
60
61 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
62 </inputs>
63 <outputs>
64 <data format="qza" label="${tool.name} on ${on_string}: distance-matrix.qza" name="odistancematrix"/>
65 </outputs>
66 <help>
67 <![CDATA[
68 Nonparametric microbial interdependence test
69 ---------------------------------------------
70
71 Perform nonparametric microbial interdependence test to determine
72 longitudinal sample similarity as a function of temporal microbial
73 composition. For more details and citation, please see
74 doi.org/10.1002/gepi.22065
75
76 Parameters
77 ----------
78 table : FeatureTable[RelativeFrequency]
79 Feature table to use for microbial interdependence test.
80 metadata : Metadata
81 Sample metadata file containing individual_id_column.
82 individual_id_column : Str
83 Metadata column containing IDs for individual subjects.
84 corr_method : Str % Choices({'kendall', 'pearson', 'spearman'}), optional
85 The temporal correlation test to be applied.
86 dist_method : Str % Choices({'fro', 'nuc'}), optional
87 Temporal distance method, see numpy.linalg.norm for details.
88
89 Returns
90 -------
91 distance_matrix : DistanceMatrix
92 The resulting distance matrix.
93 ]]>
94 </help>
95 <macros>
96 <import>qiime_citation.xml</import>
97 </macros>
98 <expand macro="qiime_citation" />
99 </tool>