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+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2018.4">
+ − 3 <description>- Collapse features by their taxonomy at the specified level</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2018.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command>
+ − 8 <![CDATA[
+ − 9 qiime taxa collapse --p-level="$plevel"
+ − 10
+ − 11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
+ − 12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
+ − 13 --i-taxonomy '$tax'
+ − 14 #else:
+ − 15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
+ − 16 --i-taxonomy '$tax'
+ − 17 #end if
+ − 18
+ − 19 --i-table=$itable --o-collapsed-table=ocollapsedtable
+ − 20 #if str($cmdconfig) != 'None':
+ − 21 --cmd-config=$cmdconfig
+ − 22 #end if
+ − 23 ;
+ − 24 cp ocollapsedtable.qza $ocollapsedtable;
+ − 25 ]]>
+ − 26 </command>
+ − 27 <inputs>
+ − 28 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data"/>
+ − 29
+ − 30 <conditional name="id_to_taxonomy_fp" optional="True">
+ − 31 <param name="selector" type="select" label="Reference taxonomy to query">
+ − 32 <option value="cached">Public databases</option>
+ − 33 <option value="history">Databases from your history</option>
+ − 34 </param>
+ − 35 <when value="cached">
+ − 36 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
+ − 37 <options from_data_table="qiime_taxonomy" />
+ − 38 </param>
+ − 39 </when>
+ − 40 <when value="history">
+ − 41 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
+ − 42 </when>
+ − 43 </conditional>
+ − 44
+ − 45 <param label="--p-level: The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" type="text"/>
+ − 46
+ − 47 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+ − 48 </inputs>
+ − 49 <outputs>
+ − 50 <data format="qza" label="${tool.name} on ${on_string}: collapsed-table.qza" name="ocollapsedtable"/>
+ − 51 </outputs>
+ − 52 <help>
+ − 53 <![CDATA[
+ − 54 Collapse features by their taxonomy at the specified level
+ − 55 -----------------------------------------------------------
+ − 56
+ − 57 Collapse groups of features that have the same taxonomic assignment through
+ − 58 the specified level. The frequencies of all features will be summed when
+ − 59 they are collapsed.
+ − 60
+ − 61 Parameters
+ − 62 ----------
+ − 63 table : FeatureTable[Frequency]
+ − 64 Feature table to be collapsed.
+ − 65 taxonomy : FeatureData[Taxonomy]
+ − 66 Taxonomic annotations for features in the provided feature table. All
+ − 67 features in the feature table must have a corresponding taxonomic
+ − 68 annotation. Taxonomic annotations that are not present in the feature
+ − 69 table will be ignored.
+ − 70 level : Int
+ − 71 The taxonomic level at which the features should be collapsed. All
+ − 72 ouput features will have exactly this many levels of taxonomic
+ − 73 annotation.
+ − 74
+ − 75 Returns
+ − 76 -------
+ − 77 collapsed_table : FeatureTable[Frequency]
+ − 78 The resulting feature table, where all features are now taxonomic
+ − 79 annotations with the user-specified number of levels.
+ − 80 ]]>
+ − 81 </help>
+ − 82 <macros>
+ − 83 <import>qiime_citation.xml</import>
+ − 84 </macros>
+ − 85 <expand macro="qiime_citation" />
+ − 86 </tool>
