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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" version="2019.4">
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3 <description> - Filter features from 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 feature-table filter-features
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9
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10 --i-table=$itable
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11
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12
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13 #if $input_files_mmetadatafile:
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14 #def list_dict_to_string(list_dict):
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15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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16 #for d in list_dict[1:]:
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17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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18 #end for
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19 #return $file_list
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20 #end def
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21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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22 #end if
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23
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24
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25 #if $pminfrequency:
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26 --p-min-frequency=$pminfrequency
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27 #end if
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28
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29 #if str($pmaxfrequency):
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30 --p-max-frequency="$pmaxfrequency"
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31 #end if
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32
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33 #if $pminsamples:
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34 --p-min-samples=$pminsamples
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35 #end if
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36
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37 #if str($pmaxsamples):
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38 --p-max-samples="$pmaxsamples"
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39 #end if
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40 --m-metadata-file=mmetadatafile
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41 #if '__sq__' in str($pwhere):
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42 #set $pwhere_temp = $pwhere.replace('__sq__', "'")
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43 #set $pwhere = $pwhere_temp
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44 #end if
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45
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46 #if str($pwhere):
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47 --p-where="$pwhere"
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48 #end if
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49
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50 #if $pexcludeids:
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51 --p-exclude-ids
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52 #end if
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53
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54 --o-filtered-table=ofilteredtable
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55 ;
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56 cp ofilteredtable.qza $ofilteredtable
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57 ]]></command>
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58 <inputs>
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59 <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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60 <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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61 <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="True" type="integer"/>
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62 <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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63 <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="True" type="integer"/>
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64 <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="True" type="text"/>
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65 <param label="--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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66
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67 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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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}: filteredtable.qza" name="ofilteredtable"/>
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74 </outputs>
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75 <help><![CDATA[
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76 Filter features from table
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77 ##########################
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78
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79 Filter features from table based on frequency and/or metadata. Any samples
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80 with a frequency of zero after feature filtering will also be removed. See
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81 the filtering tutorial on https://docs.qiime2.org for additional details.
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82
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83 Parameters
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84 ----------
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85 table : FeatureTable[Frequency]
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86 The feature table from which features should be filtered.
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87 min_frequency : Int, optional
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88 The minimum total frequency that a feature must have to be retained.
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89 max_frequency : Int, optional
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90 The maximum total frequency that a feature can have to be retained. If
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91 no value is provided this will default to infinity (i.e., no maximum
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92 frequency filter will be applied).
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93 min_samples : Int, optional
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94 The minimum number of samples that a feature must be observed in to be
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95 retained.
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96 max_samples : Int, optional
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97 The maximum number of samples that a feature can be observed in to be
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98 retained. If no value is provided this will default to infinity (i.e.,
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99 no maximum sample filter will be applied).
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100 metadata : Metadata, optional
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101 Feature metadata used with `where` parameter when selecting features to
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102 retain, or with `exclude_ids` when selecting features to discard.
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103 where : Str, optional
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104 SQLite WHERE clause specifying feature metadata criteria that must be
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105 met to be included in the filtered feature table. If not provided, all
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106 features in `metadata` that are also in the feature table will be
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107 retained.
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108 exclude_ids : Bool, optional
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109 If true, the features selected by `metadata` or `where` parameters will
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110 be excluded from the filtered table instead of being retained.
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111
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112 Returns
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113 -------
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114 filtered_table : FeatureTable[Frequency]
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115 The resulting feature table filtered by feature.
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116 ]]></help>
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117 <macros>
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118 <import>qiime_citation.xml</import>
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119 </macros>
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120 <expand macro="qiime_citation"/>
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121 </tool>
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