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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit" version="2018.4">
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3 <description> - Nonparametric microbial interdependence test</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime longitudinal nmit --i-table=$itable
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10
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11 #def list_dict_to_string(list_dict):
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12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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13 #for d in list_dict[1:]:
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14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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15 #end for
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16 #return $file_list
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17 #end def
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18
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19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-individual-id-column="$pindividualidcolumn"
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20 #if str($cmdconfig) != 'None':
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21 --cmd-config=$cmdconfig
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22 #end if
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23
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24 #if str($pdistmethod) != 'None':
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25 --p-dist-method=$pdistmethod
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26 #end if
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27
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28 #if str($pcorrmethod) != 'None':
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29 --p-corr-method=$pcorrmethod
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30 #end if
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31 --o-distance-matrix=odistancematrix;
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32
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33 cp odistancematrix.qza $odistancematrix;
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34 ]]>
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35 </command>
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36 <inputs>
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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"/>
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38
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39 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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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" />
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41 </repeat>
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42
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43 <param label="--p-individual-id-column: Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
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44
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45 <param label="--p-corr-method: The temporal correlation test to be applied.
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46 [default: kendall]" name="pcorrmethod" optional="True" type="select">
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47 <option selected="True" value="None">Selection is Optional</option>
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48 <option value="kendall">kendall</option>
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49 <option value="pearson">pearson</option>
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50 <option value="spearman">spearman</option>
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51 </param>
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52
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53 <param label="--p-dist-method: Temporal distance method, see
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54 numpy.linalg.norm for details. [default:
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55 fro]" name="pdistmethod" optional="True" type="select">
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56 <option selected="True" value="None">Selection is Optional</option>
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57 <option value="fro">fro</option>
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58 <option value="nuc">nuc</option>
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59 </param>
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60
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61 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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62 </inputs>
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63 <outputs>
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64 <data format="qza" label="${tool.name} on ${on_string}: distance-matrix.qza" name="odistancematrix"/>
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65 </outputs>
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66 <help>
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67 <![CDATA[
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68 Nonparametric microbial interdependence test
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69 ---------------------------------------------
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70
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71 Perform nonparametric microbial interdependence test to determine
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72 longitudinal sample similarity as a function of temporal microbial
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73 composition. For more details and citation, please see
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74 doi.org/10.1002/gepi.22065
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75
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76 Parameters
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77 ----------
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78 table : FeatureTable[RelativeFrequency]
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79 Feature table to use for microbial interdependence test.
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80 metadata : Metadata
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81 Sample metadata file containing individual_id_column.
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82 individual_id_column : Str
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83 Metadata column containing IDs for individual subjects.
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84 corr_method : Str % Choices({'kendall', 'pearson', 'spearman'}), optional
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85 The temporal correlation test to be applied.
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86 dist_method : Str % Choices({'fro', 'nuc'}), optional
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87 Temporal distance method, see numpy.linalg.norm for details.
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88
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89 Returns
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90 -------
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91 distance_matrix : DistanceMatrix
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92 The resulting distance matrix.
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93 ]]>
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94 </help>
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95 </tool>
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