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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-table_filter-features" name="qiime feature-table filter-features"
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3 version="2020.8">
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4 <description>Filter features from table</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 feature-table filter-features
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10
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11 --i-table=$itable
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12
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13 --p-min-frequency=$pminfrequency
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14
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15 #if str($pmaxfrequency):
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16 --p-max-frequency=$pmaxfrequency
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17 #end if
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18 --p-min-samples=$pminsamples
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19
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20 #if str($pmaxsamples):
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21 --p-max-samples=$pmaxsamples
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22 #end if# if $input_files_mmetadatafile:
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23 # def list_dict_to_string(list_dict):
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24 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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25 # for d in list_dict[1:]:
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26 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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27 # end for
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28 # return $file_list
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29 # end def
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30 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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31 # end if
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32
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33 #if '__ob__' in str($pwhere):
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34 #set $pwhere_temp = $pwhere.replace('__ob__', '[')
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35 #set $pwhere = $pwhere_temp
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36 #end if
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37 #if '__cb__' in str($pwhere):
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38 #set $pwhere_temp = $pwhere.replace('__cb__', ']')
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39 #set $pwhere = $pwhere_temp
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40 #end if
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41 #if 'X' in str($pwhere):
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42 #set $pwhere_temp = $pwhere.replace('X', '\\')
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43 #set $pwhere = $pwhere_temp
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44 #end if
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45 #if '__sq__' in str($pwhere):
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46 #set $pwhere_temp = $pwhere.replace('__sq__', "'")
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47 #set $pwhere = $pwhere_temp
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48 #end if
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49 #if '__db__' in str($pwhere):
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50 #set $pwhere_temp = $pwhere.replace('__db__', '"')
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51 #set $pwhere = $pwhere_temp
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52 #end if
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53
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54 #if str($pwhere):
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55 --p-where=$pwhere
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56 #end if
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57
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58 #if $pexcludeids:
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59 --p-exclude-ids
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60 #end if
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61
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62 --o-filtered-table=ofilteredtable
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63
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64 #if str($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 ofilteredtable.qza $ofilteredtable
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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[Frequency] The feature table from which features should be filtered. [required]" name="itable" optional="False" type="data" />
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74 <param label="--p-min-frequency: INTEGER The minimum total frequency that a feature must have to be retained. [default: 0]" name="pminfrequency" optional="True" type="integer" value="0" />
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75 <param label="--p-max-frequency: INTEGER The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]" name="pmaxfrequency" optional="False" type="text" />
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76 <param label="--p-min-samples: INTEGER The minimum number of samples that a feature must be observed in to be retained. [default: 0]" name="pminsamples" optional="True" type="integer" value="0" />
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77 <param label="--p-max-samples: INTEGER The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied). [optional]" name="pmaxsamples" optional="False" type="text" />
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78 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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79 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Feature metadata used with `where` parameter when arguments will selecting features to retain, or with `exclude-ids` be merged) when selecting features to discard. [optional]" name="additional_input" optional="True" type="data" />
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80 </repeat>
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81 <param label="--p-where: TEXT SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the feature table will be retained. [optional]" name="pwhere" optional="False" type="text" />
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82 <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids If true, the features selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean" />
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83 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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84
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85 </inputs>
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86
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87 <outputs>
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88 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable" />
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89
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90 </outputs>
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91
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92 <help><![CDATA[
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93 Filter features from table
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94 ###############################################################
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95
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96 Filter features from table based on frequency and/or metadata. Any samples
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97 with a frequency of zero after feature filtering will also be removed. See
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98 the filtering tutorial on https://docs.qiime2.org for additional details.
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99
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100 Parameters
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101 ----------
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102 table : FeatureTable[Frequency]
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103 The feature table from which features should be filtered.
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104 min_frequency : Int, optional
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105 The minimum total frequency that a feature must have to be retained.
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106 max_frequency : Int, optional
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107 The maximum total frequency that a feature can have to be retained. If
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108 no value is provided this will default to infinity (i.e., no maximum
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109 frequency filter will be applied).
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110 min_samples : Int, optional
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111 The minimum number of samples that a feature must be observed in to be
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112 retained.
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113 max_samples : Int, optional
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114 The maximum number of samples that a feature can be observed in to be
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115 retained. If no value is provided this will default to infinity (i.e.,
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116 no maximum sample filter will be applied).
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117 metadata : Metadata, optional
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118 Feature metadata used with `where` parameter when selecting features to
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119 retain, or with `exclude_ids` when selecting features to discard.
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120 where : Str, optional
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121 SQLite WHERE clause specifying feature metadata criteria that must be
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122 met to be included in the filtered feature table. If not provided, all
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123 features in `metadata` that are also in the feature table will be
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124 retained.
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125 exclude_ids : Bool, optional
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126 If true, the features selected by `metadata` or `where` parameters will
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127 be excluded from the filtered table instead of being retained.
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128
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129 Returns
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130 -------
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131 filtered_table : FeatureTable[Frequency]
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132 The resulting feature table filtered by feature.
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133 ]]></help>
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134 <macros>
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135 <import>qiime_citation.xml</import>
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136 </macros>
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137 <expand macro="qiime_citation"/>
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138 </tool> |
