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