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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" version="2019.4">
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3 <description> - Group samples or features by a metadata column</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 group
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9
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10 --i-table=$itable
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11 --p-axis=$paxis
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12 --m-metadata-column="$mmetadatacolumn"
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13 --p-mode=$pmode
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14
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15
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16 #if $input_files_mmetadatafile:
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17 #def list_dict_to_string(list_dict):
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18 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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19 #for d in list_dict[1:]:
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20 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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21 #end for
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22 #return $file_list
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23 #end def
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24 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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25 #end if
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26
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27
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28 --o-grouped-table=ogroupedtable
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29 ;
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30 cp ogroupedtable.qza $ogroupedtable
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31 ]]></command>
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32 <inputs>
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33 <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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34 <param label="--p-axis: " name="paxis" optional="False" type="select">
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35 <option value="feature">feature</option>
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36 <option value="sample">sample</option>
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37 </param>
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38 <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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39 <param label="--p-mode: " name="pmode" optional="False" type="select">
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40 <option value="median-ceiling">median-ceiling</option>
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41 <option value="mean-ceiling">mean-ceiling</option>
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42 <option value="sum">sum</option>
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43 </param>
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44
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45 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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46 <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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47 </repeat>
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48
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49 </inputs>
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50 <outputs>
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51 <data format="qza" label="${tool.name} on ${on_string}: groupedtable.qza" name="ogroupedtable"/>
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52 </outputs>
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53 <help><![CDATA[
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54 Group samples or features by a metadata column
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55 ##############################################
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56
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57 Group samples or features in a feature table using metadata to define the
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58 mapping of IDs to a group.
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59
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60 Parameters
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61 ----------
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62 table : FeatureTable[Frequency]
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63 The table to group samples or features on.
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64 axis : Str % Choices('sample', 'feature')
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65 Along which axis to group. Each ID in the given axis must exist in
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66 `metadata`.
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67 metadata : MetadataColumn[Categorical]
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68 A column defining the groups. Each unique value will become a new ID
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69 for the table on the given `axis`.
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70 mode : Str % Choices('median-ceiling', 'mean-ceiling', 'sum')
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71 How to combine samples or features within a group. `sum` will sum the
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72 frequencies across all samples or features within a group; `mean-
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73 ceiling` will take the ceiling of the mean of these frequencies;
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74 `median-ceiling` will take the ceiling of the median of these
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75 frequencies.
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76
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77 Returns
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78 -------
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79 grouped_table : FeatureTable[Frequency]
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80 A table that has been grouped along the given `axis`. IDs on that axis
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81 are replaced by values in the `metadata` column.
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82 ]]></help>
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83 <macros>
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84 <import>qiime_citation.xml</import>
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85 </macros>
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86 <expand macro="qiime_citation"/>
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87 </tool>
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