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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"
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3 version="2020.8">
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4 <description>Filter samples out of demultiplexed data.</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 demux filter-samples
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10
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11 --i-demux=$idemux
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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($input_files_mmetadatafile)
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21 # end if
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22
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23 #if '__ob__' in str($pwhere):
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24 #set $pwhere_temp = $pwhere.replace('__ob__', '[')
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25 #set $pwhere = $pwhere_temp
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26 #end if
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27 #if '__cb__' in str($pwhere):
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28 #set $pwhere_temp = $pwhere.replace('__cb__', ']')
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29 #set $pwhere = $pwhere_temp
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30 #end if
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31 #if 'X' in str($pwhere):
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32 #set $pwhere_temp = $pwhere.replace('X', '\\')
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33 #set $pwhere = $pwhere_temp
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34 #end if
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35 #if '__sq__' in str($pwhere):
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36 #set $pwhere_temp = $pwhere.replace('__sq__', "'")
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37 #set $pwhere = $pwhere_temp
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38 #end if
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39 #if '__db__' in str($pwhere):
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40 #set $pwhere_temp = $pwhere.replace('__db__', '"')
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41 #set $pwhere = $pwhere_temp
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42 #end if
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43
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44 #if str($pwhere):
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45 --p-where=$pwhere
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46 #end if
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47
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48 #if $pexcludeids:
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49 --p-exclude-ids
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50 #end if
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51
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52 --o-filtered-demux=ofiltereddemux
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53
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54 #if str($examples) != 'None':
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55 --examples=$examples
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56 #end if
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57
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58 ;
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59 cp ofiltereddemux.qza $ofiltereddemux
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60
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61 ]]></command>
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62 <inputs>
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63 <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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64 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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65 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata indicating which sample ids to filter. arguments will The optional `where` parameter may be used to filter be merged) ids based on specified conditions in the metadata. The optional `exclude-ids` parameter may be used to exclude the ids specified in the metadata from the filter. [required]" name="additional_input" optional="False" type="data" />
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66 </repeat>
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67 <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="False" type="text" />
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68 <param label="--p-exclude-ids: --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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69 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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70
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71 </inputs>
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72
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73 <outputs>
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74 <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux" />
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75
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76 </outputs>
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77
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78 <help><![CDATA[
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79 Filter samples out of demultiplexed data.
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80 ###############################################################
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81
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82 Filter samples indicated in given metadata out of demultiplexed data.
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83 Specific samples can be further selected with the WHERE clause, and the
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84 `exclude_ids` parameter allows for filtering of all samples not specified.
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85
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86 Parameters
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87 ----------
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88 demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
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89 The demultiplexed data from which samples should be filtered.
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90 metadata : Metadata
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91 Sample metadata indicating which sample ids to filter. The optional
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92 `where` parameter may be used to filter ids based on specified
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93 conditions in the metadata. The optional `exclude_ids` parameter may be
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94 used to exclude the ids specified in the metadata from the filter.
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95 where : Str, optional
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96 Optional SQLite WHERE clause specifying sample metadata criteria that
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97 must be met to be included in the filtered data. If not provided, all
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98 samples in `metadata` that are also in the demultiplexed data will be
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99 retained.
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100 exclude_ids : Bool, optional
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101 Defaults to False. If True, the samples selected by the `metadata` and
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102 optional `where` parameter will be excluded from the filtered data.
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103
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104 Returns
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105 -------
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106 filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
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107 Filtered demultiplexed data.
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108 ]]></help>
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109 <macros>
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110 <import>qiime_citation.xml</import>
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111 </macros>
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112 <expand macro="qiime_citation"/>
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113 </tool> |
