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1 <?xml version="1.0" ?>
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2 <tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2019.4">
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3 <description> - Collapse features by their taxonomy at the specified level</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 taxa collapse
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9
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6
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10 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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11 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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12 --i-taxonomy '$tax'
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13 #else:
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14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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15 --i-taxonomy '$tax'
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16 #end if
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17
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18
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19 --i-table=$itable
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6
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20
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21 #if str($plevel):
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22 --p-level="$plevel"
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23 #end if
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0
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24
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25 --o-collapsed-table=ocollapsedtable
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26 ;
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27 cp ocollapsedtable.qza $ocollapsedtable
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28 ]]></command>
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29 <inputs>
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6
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30
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31 <conditional name="id_to_taxonomy_fp" optional="True">
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32 <param name="selector" type="select" label="Reference taxonomy to query">
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33 <option value="cached">Public databases</option>
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34 <option value="history">Databases from your history</option>
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35 </param>
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36 <when value="cached">
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37 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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38 <options from_data_table="qiime_taxonomy" />
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39 </param>
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40 </when>
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41 <when value="history">
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42 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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43 </when>
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44 </conditional>
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45
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46
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47 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data"/>
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48 <param label="--p-level: INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" value="" type="integer"/>
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49 </inputs>
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50 <outputs>
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51 <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable"/>
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52 </outputs>
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53 <help><![CDATA[
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54 Collapse features by their taxonomy at the specified level
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55 ##########################################################
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56
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57 Collapse groups of features that have the same taxonomic assignment through
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58 the specified level. The frequencies of all features will be summed when
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59 they are collapsed.
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60
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61 Parameters
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62 ----------
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63 table : FeatureTable[Frequency]
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64 Feature table to be collapsed.
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65 taxonomy : FeatureData[Taxonomy]
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66 Taxonomic annotations for features in the provided feature table. All
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67 features in the feature table must have a corresponding taxonomic
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68 annotation. Taxonomic annotations that are not present in the feature
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69 table will be ignored.
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70 level : Int
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71 The taxonomic level at which the features should be collapsed. All
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72 ouput features will have exactly this many levels of taxonomic
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73 annotation.
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74
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75 Returns
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76 -------
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77 collapsed_table : FeatureTable[Frequency]
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78 The resulting feature table, where all features are now taxonomic
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79 annotations with the user-specified number of levels.
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80 ]]></help>
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81 <macros>
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82 <import>qiime_citation.xml</import>
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83 </macros>
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84 <expand macro="qiime_citation"/>
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85 </tool>
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