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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-table_filter-seqs" name="qiime feature-table filter-seqs"
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3 version="2020.8">
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4 <description>Filter features from sequences</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-seqs
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10 # if $input_files_idata:
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11 # def list_dict_to_string(list_dict):
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12 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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13 # for d in list_dict[1:]:
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14 # set $file_list = $file_list + ' --i-data=' + d['additional_input'].__getattr__('file_name')
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15 # end for
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16 # return $file_list
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17 # end def
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18 --i-data=$list_dict_to_string($input_files_idata)
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19 # end if
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20
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21 #if str($itable) != 'None':
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22 --i-table=$itable
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23 #end if
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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($input_files_mmetadatafile)
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33 # end if
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34
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35 #if '__ob__' in str($pwhere):
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36 #set $pwhere_temp = $pwhere.replace('__ob__', '[')
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37 #set $pwhere = $pwhere_temp
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38 #end if
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39 #if '__cb__' in str($pwhere):
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40 #set $pwhere_temp = $pwhere.replace('__cb__', ']')
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41 #set $pwhere = $pwhere_temp
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42 #end if
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43 #if 'X' in str($pwhere):
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44 #set $pwhere_temp = $pwhere.replace('X', '\\')
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45 #set $pwhere = $pwhere_temp
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46 #end if
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47 #if '__sq__' in str($pwhere):
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48 #set $pwhere_temp = $pwhere.replace('__sq__', "'")
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49 #set $pwhere = $pwhere_temp
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50 #end if
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51 #if '__db__' in str($pwhere):
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52 #set $pwhere_temp = $pwhere.replace('__db__', '"')
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53 #set $pwhere = $pwhere_temp
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54 #end if
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55
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56 #if str($pwhere):
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57 --p-where=$pwhere
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58 #end if
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59
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60 #if $pexcludeids:
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61 --p-exclude-ids
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62 #end if
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63
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64 --o-filtered-data=ofiltereddata
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65
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66 #if str($examples) != 'None':
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67 --examples=$examples
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68 #end if
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69
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70 ;
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71 cp ofiltereddata.qza $ofiltereddata
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72
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73 ]]></command>
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74 <inputs>
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75 <repeat name="input_files_idata" optional="False" title="--i-data">
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76 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence¹ | AlignedSequence²] The sequences from which features should be filtered. [required]" name="additional_input" optional="False" type="data" />
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77 </repeat>
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78 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Table containing feature ids used for id-based filtering. [optional]" name="itable" optional="False" type="data" />
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79 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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80 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Feature metadata used for id-based filtering, with arguments will `where` parameter when selecting features to retain, or be merged) with `exclude-ids` when selecting features to discard. [optional]" name="additional_input" optional="True" type="data" />
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81 </repeat>
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82 <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 sequences will be retained. [optional]" name="pwhere" optional="False" type="text" />
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83 <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean" />
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84 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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85
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86 </inputs>
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87
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88 <outputs>
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89 <data format="qza" label="${tool.name} on ${on_string}: filtereddata.qza" name="ofiltereddata" />
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90
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91 </outputs>
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92
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93 <help><![CDATA[
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94 Filter features from sequences
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95 ###############################################################
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96
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97 Filter features from sequences based on a feature table or metadata. See
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98 the filtering tutorial on https://docs.qiime2.org for additional details.
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99 This method can filter based on ids in a table or a metadata file, but not
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100 both (i.e., the table and metadata options are mutually exclusive).
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101
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102 Parameters
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103 ----------
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104 data : FeatureData[Sequence¹ | AlignedSequence²]
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105 The sequences from which features should be filtered.
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106 table : FeatureTable[Frequency], optional
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107 Table containing feature ids used for id-based filtering.
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108 metadata : Metadata, optional
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109 Feature metadata used for id-based filtering, with `where` parameter
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110 when selecting features to retain, or with `exclude_ids` when selecting
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111 features to discard.
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112 where : Str, optional
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113 SQLite WHERE clause specifying feature metadata criteria that must be
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114 met to be included in the filtered feature table. If not provided, all
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115 features in `metadata` that are also in the sequences will be retained.
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116 exclude_ids : Bool, optional
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117 If true, the features selected by the `metadata` (with or without the
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118 `where` parameter) or `table` parameter will be excluded from the
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119 filtered sequences instead of being retained.
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120
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121 Returns
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122 -------
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123 filtered_data : FeatureData[Sequence¹ | AlignedSequence²]
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124 The resulting filtered sequences.
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125 ]]></help>
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126 <macros>
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127 <import>qiime_citation.xml</import>
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128 </macros>
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129 <expand macro="qiime_citation"/>
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130 </tool> |