diff qiime2/qiime_fragment-insertion_classify-otus-experimental.xml @ 29:3ba9833030c1 draft

Uploaded

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+++ b/qiime2/qiime_fragment-insertion_classify-otus-experimental.xml	Fri Sep 04 13:12:49 2020 +0000
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+<?xml version="1.0" ?>
+<tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental"
+      version="2020.8">
+  <description>Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime fragment-insertion classify-otus-experimental
+
+--i-representative-sequences=$irepresentativesequences
+
+--i-tree=$itree
+
+--i-reference-taxonomy=$ireferencetaxonomy
+
+--o-classification=oclassification
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp oclassification.qza $oclassification
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences used for a \'sepp\' run to produce the \'tree\'.                                      [required]" name="irepresentativesequences" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT    The tree resulting from inserting fragments into a Phylogeny[Rooted]  reference phylogeny, i.e. the output of function \'sepp\' [required]" name="itree" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string.                  [required]" name="ireferencetaxonomy" optional="False" type="data" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.
+###############################################################
+
+
+Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
+for every inserted fragment. Then, look up the reference lineage string in
+the reference taxonomy.
+
+Parameters
+----------
+representative_sequences : FeatureData[Sequence]
+    The sequences used for a 'sepp' run to produce the 'tree'.
+tree : Phylogeny[Rooted]
+    The tree resulting from inserting fragments into a reference phylogeny,
+    i.e. the output of function 'sepp'
+reference_taxonomy : FeatureData[Taxonomy]
+    Reference taxonomic table that maps every OTU-ID into a taxonomic
+    lineage string.
+
+Returns
+-------
+classification : FeatureData[Taxonomy]
+    Taxonomic lineages for inserted fragments.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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