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1 <?xml version="1.0" ?>
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2 <tool id="qiime_sample-classifier_split-table" name="qiime sample-classifier split-table"
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3 version="2020.8">
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4 <description>Split a feature table into training and testing sets.</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 sample-classifier split-table
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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($input_files_mmetadatafile)
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21 # end if
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22
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23 #if '__ob__' in str($mmetadatacolumn):
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24 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
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25 #set $mmetadatacolumn = $mmetadatacolumn_temp
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26 #end if
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27 #if '__cb__' in str($mmetadatacolumn):
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28 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
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29 #set $mmetadatacolumn = $mmetadatacolumn_temp
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30 #end if
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31 #if 'X' in str($mmetadatacolumn):
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32 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
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33 #set $mmetadatacolumn = $mmetadatacolumn_temp
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34 #end if
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35 #if '__sq__' in str($mmetadatacolumn):
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36 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
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37 #set $mmetadatacolumn = $mmetadatacolumn_temp
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38 #end if
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39 #if '__db__' in str($mmetadatacolumn):
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40 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
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41 #set $mmetadatacolumn = $mmetadatacolumn_temp
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42 #end if
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43
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44 --m-metadata-column=$mmetadatacolumn
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45
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46
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47 --p-test-size=$ptestsize
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48
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49 #if str($prandomstate):
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50 --p-random-state=$prandomstate
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51 #end if
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52 #if $pnostratify:
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53 --p-no-stratify
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54 #end if
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55
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56 #if str($pmissingsamples) != 'None':
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57 --p-missing-samples=$pmissingsamples
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58 #end if
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59
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60 --o-training-table=otrainingtable
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61
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62 --o-test-table=otesttable
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63
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64 #if str($examples) != 'None':
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65 --examples=$examples
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66 #end if
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67
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68 ;
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69 cp otesttable.qza $otesttable
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70
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71 ]]></command>
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72 <inputs>
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73 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶] Feature table containing all features that should be used for target prediction. [required]" name="itable" optional="False" type="data" />
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74 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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75 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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76 </repeat>
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77 <param label="--m-metadata-column: COLUMN MetadataColumn[Numeric | Categorical] Numeric metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text" />
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78 <param exclude_min="True" label="--p-test-size: PROPORTION Range(0.0, 1.0, inclusive_start=False) Fraction of input samples to exclude from training set and use for classifier testing. [default: 0.2]" max="1.0" min="0.0" name="ptestsize" optional="True" type="float" value="0.2" />
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79 <param label="--p-random-state: INTEGER Seed used by random number generator. [optional]" name="prandomstate" optional="False" type="text" />
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80 <param label="--p-no-stratify: Do not evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: True]" name="pnostratify" selected="False" type="boolean" />
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81 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
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82 <option selected="True" value="None">Selection is Optional</option>
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83 <option value="error">error</option>
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84 <option value="ignore">ignore</option>
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85 </param>
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86 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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87
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88 </inputs>
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89
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90 <outputs>
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91 <data format="qza" label="${tool.name} on ${on_string}: trainingtable.qza" name="otrainingtable" />
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92 <data format="qza" label="${tool.name} on ${on_string}: testtable.qza" name="otesttable" />
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93
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94 </outputs>
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95
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96 <help><![CDATA[
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97 Split a feature table into training and testing sets.
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98 ###############################################################
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99
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100 Split a feature table into training and testing sets. By default stratifies
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101 training and test sets on a metadata column, such that values in that
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102 column are evenly represented across training and test sets.
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103
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104 Parameters
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105 ----------
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106 table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶]
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107 Feature table containing all features that should be used for target
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108 prediction.
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109 metadata : MetadataColumn[Numeric | Categorical]
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110 Numeric metadata column to use as prediction target.
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111 test_size : Float % Range(0.0, 1.0, inclusive_start=False), optional
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112 Fraction of input samples to exclude from training set and use for
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113 classifier testing.
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114 random_state : Int, optional
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115 Seed used by random number generator.
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116 stratify : Bool, optional
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117 Evenly stratify training and test data among metadata categories. If
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118 True, all values in column must match at least two samples.
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119 missing_samples : Str % Choices('error', 'ignore'), optional
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120 How to handle missing samples in metadata. "error" will fail if missing
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121 samples are detected. "ignore" will cause the feature table and
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122 metadata to be filtered, so that only samples found in both files are
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123 retained.
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124
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125 Returns
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126 -------
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127 training_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶]
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128 Feature table containing training samples
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129 test_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶]
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130 Feature table containing test samples
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131 ]]></help>
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132 <macros>
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133 <import>qiime_citation.xml</import>
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134 </macros>
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135 <expand macro="qiime_citation"/>
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136 </tool> |
