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1 <?xml version="1.0" ?>
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2 <tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime taxa collapse --p-level="$plevel"
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10
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11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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13 --i-taxonomy '$tax'
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14 #else:
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15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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16 --i-taxonomy '$tax'
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17 #end if
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18
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19 --i-table=$itable --o-collapsed-table=ocollapsedtable
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20 #if str($cmdconfig) != 'None':
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21 --cmd-config=$cmdconfig
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22 #end if
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23 ;
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24 cp ocollapsedtable.qza $ocollapsedtable;
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data"/>
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29
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30 <conditional name="id_to_taxonomy_fp" optional="True">
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31 <param name="selector" type="select" label="Reference taxonomy to query">
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32 <option value="cached">Public databases</option>
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33 <option value="history">Databases from your history</option>
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34 </param>
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35 <when value="cached">
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36 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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37 <options from_data_table="qiime_taxonomy" />
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38 </param>
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39 </when>
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40 <when value="history">
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41 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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42 </when>
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43 </conditional>
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44
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45 <param label="--p-level: 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" type="text"/>
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46
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47 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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48 </inputs>
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49 <outputs>
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50 <data format="qza" label="${tool.name} on ${on_string}: collapsed-table.qza" name="ocollapsedtable"/>
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51 </outputs>
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52 <help>
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53 <![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 ]]>
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81 </help>
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82 <macros>
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83 <import>qiime_citation.xml</import>
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84 </macros>
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85 <expand macro="qiime_citation" />
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86 </tool>
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