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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-table_group" name="qiime feature-table group"
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3 version="2020.8">
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4 <description>Group samples or features by a metadata column</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 group
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10
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11 --i-table=$itable
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12
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13 --p-axis=$paxis
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14 # if $input_files_mmetadatafile:
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15 # def list_dict_to_string(list_dict):
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16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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17 # for d in list_dict[1:]:
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18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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19 # end for
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20 # return $file_list
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21 # end def
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22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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23 # end if
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24
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25 #if '__ob__' in str($mmetadatacolumn):
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26 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
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27 #set $mmetadatacolumn = $mmetadatacolumn_temp
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28 #end if
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29 #if '__cb__' in str($mmetadatacolumn):
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30 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
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31 #set $mmetadatacolumn = $mmetadatacolumn_temp
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32 #end if
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33 #if 'X' in str($mmetadatacolumn):
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34 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
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35 #set $mmetadatacolumn = $mmetadatacolumn_temp
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36 #end if
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37 #if '__sq__' in str($mmetadatacolumn):
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38 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
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39 #set $mmetadatacolumn = $mmetadatacolumn_temp
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40 #end if
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41 #if '__db__' in str($mmetadatacolumn):
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42 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
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43 #set $mmetadatacolumn = $mmetadatacolumn_temp
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44 #end if
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45
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46 --m-metadata-column=$mmetadatacolumn
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47
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48
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49 --p-mode=$pmode
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50
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51 --o-grouped-table=ogroupedtable
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52
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53 #if str($examples) != 'None':
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54 --examples=$examples
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55 #end if
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56
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57 ;
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58 cp ogroupedtable.qza $ogroupedtable
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59
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60 ]]></command>
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61 <inputs>
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62 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The table to group samples or features on. [required]" name="itable" optional="False" type="data" />
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63 <param label="--p-axis: " name="paxis" optional="False" type="select">
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64 <option value="sample">sample</option>
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65 <option value="feature">feature</option>
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66 </param>
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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 column defining the groups. Each unique value will become a new ID for the table on the given `axis`. [required]" name="mmetadatacolumn" optional="False" type="text" />
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71 <param label="--p-mode: " name="pmode" optional="False" type="select">
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72 <option value="sum">sum</option>
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73 <option value="mean-ceiling">mean-ceiling</option>
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74 <option value="median-ceiling">median-ceiling</option>
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75 </param>
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76 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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77
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78 </inputs>
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79
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80 <outputs>
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81 <data format="qza" label="${tool.name} on ${on_string}: groupedtable.qza" name="ogroupedtable" />
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82
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83 </outputs>
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84
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85 <help><![CDATA[
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86 Group samples or features by a metadata column
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87 ###############################################################
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88
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89 Group samples or features in a feature table using metadata to define the
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90 mapping of IDs to a group.
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91
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92 Parameters
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93 ----------
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94 table : FeatureTable[Frequency]
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95 The table to group samples or features on.
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96 axis : Str % Choices('sample', 'feature')
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97 Along which axis to group. Each ID in the given axis must exist in
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98 `metadata`.
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99 metadata : MetadataColumn[Categorical]
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100 A column defining the groups. Each unique value will become a new ID
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101 for the table on the given `axis`.
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102 mode : Str % Choices('sum', 'mean-ceiling', 'median-ceiling')
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103 How to combine samples or features within a group. `sum` will sum the
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104 frequencies across all samples or features within a group; `mean-
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105 ceiling` will take the ceiling of the mean of these frequencies;
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106 `median-ceiling` will take the ceiling of the median of these
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107 frequencies.
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108
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109 Returns
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110 -------
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111 grouped_table : FeatureTable[Frequency]
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112 A table that has been grouped along the given `axis`. IDs on that axis
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113 are replaced by values in the `metadata` column.
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114 ]]></help>
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115 <macros>
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116 <import>qiime_citation.xml</import>
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117 </macros>
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118 <expand macro="qiime_citation"/>
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119 </tool> |
