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1 <?xml version="1.0" ?>
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2 <tool id="qiime_sample-classifier_metatable" name="qiime sample-classifier metatable" version="2019.4">
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3 <description> - Convert (and merge) positive numeric metadata (in)to feature table.</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 sample-classifier metatable
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9
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10
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11 #if str($itable) != 'None':
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12 --i-table=$itable
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13 #end if
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14
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15 #if str($pmissingsamples) != 'None':
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16 --p-missing-samples=$pmissingsamples
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17 #end if
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18
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19 #if str($pmissingvalues) != 'None':
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20 --p-missing-values=$pmissingvalues
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21 #end if
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22
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23
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24 #if $input_files_mmetadatafile:
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25 #def list_dict_to_string(list_dict):
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26 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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27 #for d in list_dict[1:]:
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28 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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29 #end for
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30 #return $file_list
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31 #end def
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32 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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33 #end if
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34
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35
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36 --o-converted-table=oconvertedtable
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37 ;
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38 cp oconvertedtable.qza $oconvertedtable
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39 ]]></command>
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40 <inputs>
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41 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction. [optional]" name="itable" optional="True" type="data"/>
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42 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
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43 <option selected="True" value="None">Selection is Optional</option>
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44 <option value="error">error</option>
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45 <option value="ignore">ignore</option>
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46 </param>
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47 <param label="--p-missing-values: " name="pmissingvalues" optional="True" type="select">
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48 <option selected="True" value="None">Selection is Optional</option>
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49 <option value="drop_samples">drop_samples</option>
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50 <option value="drop_features">drop_features</option>
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51 <option value="error">error</option>
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52 <option value="fill">fill</option>
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53 </param>
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54
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55 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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56 <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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57 </repeat>
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58
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59 </inputs>
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60 <outputs>
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61 <data format="qza" label="${tool.name} on ${on_string}: convertedtable.qza" name="oconvertedtable"/>
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62 </outputs>
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63 <help><![CDATA[
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64 Convert (and merge) positive numeric metadata (in)to feature table.
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65 ###################################################################
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66
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67 Convert numeric sample metadata from TSV file into a feature table.
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68 Optionally merge with an existing feature table. Only numeric metadata will
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69 be converted; categorical columns will be silently dropped. By default, if
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70 a table is used as input only samples found in both the table and metadata
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71 (intersection) are merged, and others are silently dropped. Set
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72 missing_samples="error" to raise an error if samples found in the table are
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73 missing from the metadata file. The metadata file can always contain a
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74 superset of samples. Note that columns will be dropped if they are non-
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75 numeric, contain only unique values, contain no unique values (zero
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76 variance), contain only empty cells, or contain negative values. This
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77 method currently only converts postive numeric metadata into feature data.
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78 Tip: convert categorical columns to dummy variables to include them in the
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79 output feature table.
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80
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81 Parameters
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82 ----------
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83 metadata : Metadata
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84 Metadata file to convert to feature table.
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85 table : FeatureTable[Frequency], optional
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86 Feature table containing all features that should be used for target
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87 prediction.
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88 missing_samples : Str % Choices('error', 'ignore'), optional
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89 How to handle missing samples in metadata. "error" will fail if missing
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90 samples are detected. "ignore" will cause the feature table and
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91 metadata to be filtered, so that only samples found in both files are
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92 retained.
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93 missing_values : Str % Choices('drop_samples', 'drop_features', 'error', 'fill'), optional
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94 How to handle missing values (nans) in metadata. Either "drop_samples"
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95 with missing values, "drop_features" with missing values, "fill"
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96 missing values with zeros, or "error" if any missing values are found.
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97
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98 Returns
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99 -------
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100 converted_table : FeatureTable[Frequency]
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101 Converted feature table
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102 ]]></help>
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103 <macros>
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104 <import>qiime_citation.xml</import>
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105 </macros>
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106 <expand macro="qiime_citation"/>
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107 </tool>
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