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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_filter-distance-matrix" name="qiime diversity filter-distance-matrix" version="2019.4">
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3 <description> - Filter samples from a distance matrix.</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 diversity filter-distance-matrix
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9
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10 --i-distance-matrix=$idistancematrix
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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($input_files_mmetadatafile)
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22 #end if
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23
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24
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25 #if '__sq__' in str($pwhere):
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26 #set $pwhere_temp = $pwhere.replace('__sq__', "'")
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27 #set $pwhere = $pwhere_temp
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28 #end if
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29
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30 #if str($pwhere):
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31 --p-where="$pwhere"
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32 #end if
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33
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34
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35 #if $pexcludeids:
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36 --p-exclude-ids
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37 #end if
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38
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39 --o-filtered-distance-matrix=ofiltereddistancematrix
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40 ;
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41 cp ofiltereddistancematrix.qza $ofiltereddistancematrix
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42 ]]></command>
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43 <inputs>
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44 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Distance matrix to filter by sample. [required]" name="idistancematrix" optional="False" type="data"/>
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45 <param label="--p-where: TEXT SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained. [optional]" name="pwhere" optional="True" type="text"/>
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46 <param label="--p-exclude-ids: --p-no-exclude-ids If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean"/>
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47
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48 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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49 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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50 </repeat>
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51
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52 </inputs>
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53 <outputs>
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54 <data format="qza" label="${tool.name} on ${on_string}: filtereddistancematrix.qza" name="ofiltereddistancematrix"/>
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55 </outputs>
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56 <help><![CDATA[
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57 Filter samples from a distance matrix.
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58 ######################################
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59
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60 Filter samples from a distance matrix, retaining only the samples matching
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61 search criteria specified by `metadata` and `where` parameters (or
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62 retaining only the samples not matching that criteria, if `exclude_ids` is
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63 True). See the filtering tutorial on https://docs.qiime2.org for additional
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64 details.
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65
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66 Parameters
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67 ----------
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68 distance_matrix : DistanceMatrix
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69 Distance matrix to filter by sample.
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70 metadata : Metadata
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71 Sample metadata used with `where` parameter when selecting samples to
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72 retain, or with `exclude_ids` when selecting samples to discard.
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73 where : Str, optional
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74 SQLite WHERE clause specifying sample metadata criteria that must be
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75 met to be included in the filtered distance matrix. If not provided,
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76 all samples in `metadata` that are also in the input distance matrix
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77 will be retained.
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78 exclude_ids : Bool, optional
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79 If `True`, the samples selected by `metadata` or `where` parameters
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80 will be excluded from the filtered distance matrix instead of being
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81 retained.
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82
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83 Returns
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84 -------
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85 filtered_distance_matrix : DistanceMatrix
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86 Distance matrix filtered to include samples matching search criteria
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87 ]]></help>
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88 <macros>
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89 <import>qiime_citation.xml</import>
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90 </macros>
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91 <expand macro="qiime_citation"/>
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92 </tool>
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