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

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental"
3 version="2020.8">
4 <description>Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime fragment-insertion classify-otus-experimental
10
11 --i-representative-sequences=$irepresentativesequences
12
13 --i-tree=$itree
14
15 --i-reference-taxonomy=$ireferencetaxonomy
16
17 --o-classification=oclassification
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
23 ;
24 cp oclassification.qza $oclassification
25
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences used for a \'sepp\' run to produce the \'tree\'. [required]" name="irepresentativesequences" optional="False" type="data" />
29 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree resulting from inserting fragments into a Phylogeny[Rooted] reference phylogeny, i.e. the output of function \'sepp\' [required]" name="itree" optional="False" type="data" />
30 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string. [required]" name="ireferencetaxonomy" optional="False" type="data" />
31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
32
33 </inputs>
34
35 <outputs>
36 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
37
38 </outputs>
39
40 <help><![CDATA[
41 Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.
42 ###############################################################
43
44
45 Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
46 for every inserted fragment. Then, look up the reference lineage string in
47 the reference taxonomy.
48
49 Parameters
50 ----------
51 representative_sequences : FeatureData[Sequence]
52 The sequences used for a 'sepp' run to produce the 'tree'.
53 tree : Phylogeny[Rooted]
54 The tree resulting from inserting fragments into a reference phylogeny,
55 i.e. the output of function 'sepp'
56 reference_taxonomy : FeatureData[Taxonomy]
57 Reference taxonomic table that maps every OTU-ID into a taxonomic
58 lineage string.
59
60 Returns
61 -------
62 classification : FeatureData[Taxonomy]
63 Taxonomic lineages for inserted fragments.
64 ]]></help>
65 <macros>
66 <import>qiime_citation.xml</import>
67 </macros>
68 <expand macro="qiime_citation"/>
69 </tool>