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1 <?xml version="1.0" ?>
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2 <tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" version="2019.7">
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3 <description> - Filter samples out of demultiplexed data.</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime demux filter-samples
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9
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10 --i-demux=$idemux
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11
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12
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13 #if $input_files_mmetadatafile:
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14 #def list_dict_to_string(list_dict):
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15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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16 #for d in list_dict[1:]:
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17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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18 #end for
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19 #return $file_list
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20 #end def
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21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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22 #end if
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23
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24
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25
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26 #if '__sq__' in str($pwhere):
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27 #set $pwhere_temp = $pwhere.replace('__sq__', "'")
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28 #set $pwhere = $pwhere_temp
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29 #end if
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30
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31
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32 #if str($pwhere):
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33 --p-where="$pwhere"
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34 #end if
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35
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36
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37 #if $pexcludeids:
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38 --p-exclude-ids
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39 #end if
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40
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41
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42 --o-filtered-demux=ofiltereddemux
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43
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44 ;
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45 cp ofiltereddemux.qza $ofiltereddemux
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46 ]]></command>
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47 <inputs>
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48
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49 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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50 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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51 </repeat>
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52
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53 <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered. [required]" name="idemux" optional="False" type="data"/>
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54 <param label="--p-where: TEXT Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]" name="pwhere" optional="True" type="text"/>
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55 <param label="--p-exclude-ids: --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]" name="pexcludeids" selected="False" type="boolean"/>
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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}: filtereddemux.qza" name="ofiltereddemux"/>
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59 </outputs>
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60 <help><![CDATA[
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61 Filter samples out of demultiplexed data.
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62 #########################################
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63
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64 Filter samples indicated in given metadata out of demultiplexed data.
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65 Specific samples can be further selected with the WHERE clause, and the
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66 `exclude_ids` parameter allows for filtering of all samples not specified.
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67
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68 Parameters
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69 ----------
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70 demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
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71 The demultiplexed data from which samples should be filtered.
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72 metadata : Metadata
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73 Sample metadata indicating which sample ids to filter. The optional
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74 `where` parameter may be used to filter ids based on specified
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75 conditions in the metadata. The optional `exclude_ids` parameter may be
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76 used to exclude the ids specified in the metadata from the filter.
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77 where : Str, optional
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78 Optional SQLite WHERE clause specifying sample metadata criteria that
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79 must be met to be included in the filtered data. If not provided, all
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80 samples in `metadata` that are also in the demultiplexed data will be
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81 retained.
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82 exclude_ids : Bool, optional
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83 Defaults to False. If True, the samples selected by the `metadata` and
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84 optional `where` parameter will be excluded from the filtered data.
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85
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86 Returns
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87 -------
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88 filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
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89 Filtered demultiplexed data.
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90 ]]></help>
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91 <macros>
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92 <import>qiime_citation.xml</import>
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93 </macros>
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94 <expand macro="qiime_citation"/>
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95 </tool>
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