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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 $pexcludeids:
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38 --p-exclude-ids
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39 #end if
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40
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41 #if str($citations) != 'None':
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42 --citations=$citations
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43 #end if
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44
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45
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46 --o-filtered-demux=ofiltereddemux
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47
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48 ;
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49 cp ofiltereddemux.qza $ofiltereddemux
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50 ]]></command>
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51 <inputs>
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52
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53 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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54 <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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55 </repeat>
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56
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57 <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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58 <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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59 <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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60 </inputs>
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61 <outputs>
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62 <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux"/>
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63 </outputs>
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64 <help><![CDATA[
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65
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66 ]]></help>
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67 <macros>
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68 <import>qiime_citation.xml</import>
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69 </macros>
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70 <expand macro="qiime_citation"/>
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71 </tool>
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