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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit" version="2019.4">
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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="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime longitudinal nmit
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9
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10 --i-table=$itable
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4
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11
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12
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13
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14
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15 #if '__sq__' in str($pindividualidcolumn):
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16 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
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17 #set $pindividualidcolumn = $pindividualidcolumn_temp
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18 #end if
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19
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20 #if str($pindividualidcolumn):
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21 --p-individual-id-column="$pindividualidcolumn"
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22 #end if
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23
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24
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25
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0
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26
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27 #if str($pcorrmethod) != 'None':
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28 --p-corr-method=$pcorrmethod
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29 #end if
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30
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31 #if str($pdistmethod) != 'None':
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32 --p-dist-method=$pdistmethod
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33 #end if
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34
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35
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36 #if $input_files_mmetadatafile:
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37 #def list_dict_to_string(list_dict):
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38 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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39 #for d in list_dict[1:]:
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40 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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41 #end for
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42 #return $file_list
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43 #end def
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44 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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45 #end if
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46
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47
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48 --o-distance-matrix=odistancematrix
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49 ;
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50 cp odistancematrix.qza $odistancematrix
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51 ]]></command>
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52 <inputs>
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53 <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"/>
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54 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
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55 <param label="--p-corr-method: " name="pcorrmethod" 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="kendall">kendall</option>
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58 <option value="pearson">pearson</option>
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59 <option value="spearman">spearman</option>
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60 </param>
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61 <param label="--p-dist-method: " name="pdistmethod" optional="True" type="select">
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62 <option selected="True" value="None">Selection is Optional</option>
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63 <option value="fro">fro</option>
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64 <option value="nuc">nuc</option>
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65 </param>
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66
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67 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
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68 <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" />
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69 </repeat>
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70
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71 </inputs>
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72 <outputs>
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73 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/>
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74 </outputs>
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75 <help><![CDATA[
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76 Nonparametric microbial interdependence test
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77 ############################################
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78
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79 Perform nonparametric microbial interdependence test to determine
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80 longitudinal sample similarity as a function of temporal microbial
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81 composition. For more details and citation, please see
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82 doi.org/10.1002/gepi.22065
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83
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84 Parameters
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85 ----------
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86 table : FeatureTable[RelativeFrequency]
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87 Feature table to use for microbial interdependence test.
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88 metadata : Metadata
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89 Sample metadata file containing individual_id_column.
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90 individual_id_column : Str
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91 Metadata column containing IDs for individual subjects.
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92 corr_method : Str % Choices('kendall', 'pearson', 'spearman'), optional
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93 The temporal correlation test to be applied.
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94 dist_method : Str % Choices('fro', 'nuc'), optional
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95 Temporal distance method, see numpy.linalg.norm for details.
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96
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97 Returns
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98 -------
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99 distance_matrix : DistanceMatrix
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100 The resulting distance matrix.
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101 ]]></help>
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102 <macros>
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103 <import>qiime_citation.xml</import>
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104 </macros>
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105 <expand macro="qiime_citation"/>
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106 </tool>
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