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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-table_tabulate-seqs" name="qiime feature-table tabulate-seqs"
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3 version="2020.8">
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4 <description>View sequence associated with each feature</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 feature-table tabulate-seqs
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10 # if $input_files_idata:
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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 + ' --i-data=' + d['additional_input'].__getattr__('file_name')
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15 # end for
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16 # return $file_list
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17 # end def
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18 --i-data=$list_dict_to_string($input_files_idata)
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19 # end if
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20
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21 --o-visualization=ovisualization
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22
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23 #if str($examples) != 'None':
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24 --examples=$examples
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25 #end if
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26
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27 ;
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28 cp osampledtable.qza $osampledtable
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29
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30 ;
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31 qiime tools export ovisualization.qzv --output-path out
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32 && mkdir -p '$ovisualization.files_path'
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33 && cp -r out/* '$ovisualization.files_path'
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34 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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35
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36 ;
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37 qiime tools export ovisualization.qzv --output-path out
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38 && mkdir -p '$ovisualization.files_path'
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39 && cp -r out/* '$ovisualization.files_path'
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40 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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41
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42 ]]></command>
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43 <inputs>
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44 <repeat name="input_files_idata" optional="False" title="--i-data">
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45 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required]" name="additional_input" optional="False" type="data" />
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46 </repeat>
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47 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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48
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49 </inputs>
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50
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51 <outputs>
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52 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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53
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54 </outputs>
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55
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56 <help><![CDATA[
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57 View sequence associated with each feature
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58 ###############################################################
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59
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60 Generate tabular view of feature identifier to sequence mapping, including
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61 links to BLAST each sequence against the NCBI nt database.
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62
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63 Parameters
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64 ----------
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65 data : FeatureData[Sequence | AlignedSequence]
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66 The feature sequences to be tabulated.
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67
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68 Returns
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69 -------
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70 visualization : Visualization
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71 ]]></help>
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72 <macros>
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73 <import>qiime_citation.xml</import>
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74 </macros>
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75 <expand macro="qiime_citation"/>
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76 </tool> |
