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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="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime feature-table group --i-table=$itable
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10
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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 + ',' + d['additional_input'].__getattr__('file_name')
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15 #end for
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16 #return $file_list
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17
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18 #end def
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19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-mode=$pmode --m-metadata-column="$mmetadatacolumn" --p-axis=$paxis
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20 #if str($cmdconfig) != 'None':
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21 --cmd-config=$cmdconfig
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22 #end if
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23 --o-grouped-table=ogroupedtable;
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24 cp ogroupedtable.qza $ogroupedtable;
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The table to group samples or features on. [required]" name="itable" optional="False" type="data"/>
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29
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30 <param label="--p-axis: Along which axis to group. Each ID in the
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31 given axis must exist in `metadata`.
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32 [required]" name="paxis" optional="False" type="select">
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33 <option value="sample">sample</option>
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34 <option value="feature">feature</option>
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35 </param>
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36
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37 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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38 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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39 </repeat>
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40
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41 <param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. 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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42
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43 <param label="--p-mode: How to combine samples or features within a
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44 group. `sum` will sum the frequencies across
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45 all samples or features within a group;
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46 `mean-ceiling` will take the ceiling of the
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47 mean of these frequencies; `median-ceiling`
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48 will take the ceiling of the median of these
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49 frequencies. [required]" name="pmode" optional="False" type="select">
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50 <option value="median-ceiling">median-ceiling</option>
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51 <option value="mean-ceiling">mean-ceiling</option>
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52 <option value="sum">sum</option>
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53 </param>
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54
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55 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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56 </inputs>
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57 <outputs>
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58 <data format="qza" label="${tool.name} on ${on_string}: grouped-table.qza" name="ogroupedtable"/>
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59 </outputs>
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60 <help>
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61 <![CDATA[
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62 Group samples or features by a metadata column
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63 -----------------------------------------------
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64
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65 Group samples or features in a feature table using metadata to define the
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66 mapping of IDs to a group.
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67
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68 Parameters
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69 ----------
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70 table : FeatureTable[Frequency]
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71 The table to group samples or features on.
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72 axis : Str % Choices({'feature', 'sample'})
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73 Along which axis to group. Each ID in the given axis must exist in
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74 `metadata`.
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75 metadata : MetadataColumn[Categorical]
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76 A column defining the groups. Each unique value will become a new ID
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77 for the table on the given `axis`.
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78 mode : Str % Choices({'mean-ceiling', 'median-ceiling', 'sum'})
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79 How to combine samples or features within a group. `sum` will sum the
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80 frequencies across all samples or features within a group; `mean-
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81 ceiling` will take the ceiling of the mean of these frequencies;
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82 `median-ceiling` will take the ceiling of the median of these
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83 frequencies.
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84
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85 Returns
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86 -------
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87 grouped_table : FeatureTable[Frequency]
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88 A table that has been grouped along the given `axis`. IDs on that axis
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89 are replaced by values in the `metadata` column.
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90 ]]>
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91 </help>
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92 </tool>
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