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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-table_rename-ids" name="qiime feature-table rename-ids"
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3 version="2020.8">
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4 <description>Renames sample or feature ids in a 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 rename-ids
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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 #if str($paxis) != 'None':
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48 --p-axis=$paxis
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49 #end if
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50
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51 #if $pstrict:
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52 --p-strict
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53 #end if
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54
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55 --o-renamed-table=orenamedtable
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56
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57 #if str($examples) != 'None':
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58 --examples=$examples
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59 #end if
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60
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61 ;
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62 cp orenamedtable.qza $orenamedtable
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63
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64 ]]></command>
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65 <inputs>
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66 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴] The table to be renamed [required]" name="itable" optional="False" type="data" />
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67 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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68 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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69 </repeat>
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70 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] A metadata column defining the new ids. Each original id must map to a new unique id. If strict mode is used, then every id in the original table must have a new id. [required]" name="mmetadatacolumn" optional="False" type="text" />
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71 <param label="--p-axis: " name="paxis" optional="True" type="select">
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72 <option selected="True" value="None">Selection is Optional</option>
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73 <option value="sample">sample</option>
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74 <option value="feature">feature</option>
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75 </param>
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76 <param label="--p-strict: --p-strict: / --p-no-strict Whether the naming needs to be strict (each id in the table must have a new id). Otherwise, only the ids described in `metadata` will be renamed and the others will keep their original id names. [default: False]" name="pstrict" selected="False" type="boolean" />
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77 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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78
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79 </inputs>
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80
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81 <outputs>
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82 <data format="qza" label="${tool.name} on ${on_string}: renamedtable.qza" name="orenamedtable" />
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83
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84 </outputs>
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85
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86 <help><![CDATA[
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87 Renames sample or feature ids in a table
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88 ###############################################################
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89
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90 Renames the sample or feature ids in a feature table using metadata to
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91 define the new ids.
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92
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93 Parameters
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94 ----------
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95 table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
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96 The table to be renamed
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97 metadata : MetadataColumn[Categorical]
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98 A metadata column defining the new ids. Each original id must map to a
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99 new unique id. If strict mode is used, then every id in the original
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100 table must have a new id.
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101 axis : Str % Choices('sample', 'feature'), optional
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102 Along which axis to rename the ids.
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103 strict : Bool, optional
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104 Whether the naming needs to be strict (each id in the table must have a
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105 new id). Otherwise, only the ids described in `metadata` will be
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106 renamed and the others will keep their original id names.
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107
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108 Returns
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109 -------
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110 renamed_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
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111 A table which has new ids, where the ids are replaced by values in the
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112 `metadata` column.
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113 ]]></help>
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114 <macros>
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115 <import>qiime_citation.xml</import>
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116 </macros>
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117 <expand macro="qiime_citation"/>
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118 </tool> |
