|
0
|
1 <?xml version="1.0" ?>
|
|
9
|
2 <tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental" version="2019.7">
|
|
0
|
3 <description> - Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
|
|
|
4 <requirements>
|
|
9
|
5 <requirement type="package" version="2019.7">qiime2</requirement>
|
|
0
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime fragment-insertion classify-otus-experimental
|
|
|
9
|
|
|
10 --i-representative-sequences=$irepresentativesequences
|
|
|
11 --i-tree=$itree --o-classification=oclassification
|
|
|
12
|
|
|
13
|
|
|
14 #if str( $id_to_taxonomy_fp.selector ) == 'history'
|
|
|
15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
|
|
|
16 --i-reference-taxonomy '$tax'
|
|
|
17 #else:
|
|
|
18 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
|
|
|
19 --i-reference-taxonomy '$tax'
|
|
|
20 #end if
|
|
|
21
|
|
|
22
|
|
|
23 ;
|
|
|
24 cp oclassification.qza $oclassification
|
|
|
25 ]]></command>
|
|
|
26 <inputs>
|
|
|
27 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences used for a 'sepp' run to produce the 'tree'. [required]" name="irepresentativesequences" optional="False" type="data"/>
|
|
|
28 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree resulting from inserting fragments into a Phylogeny[Rooted] reference phylogeny, i.e. the output of function 'sepp' [required]" name="itree" optional="False" type="data"/>
|
|
|
29
|
|
|
30 <conditional name="id_to_taxonomy_fp" optional="True">
|
|
|
31 <param name="selector" type="select" label="Reference taxonomy to query">
|
|
|
32 <option value="cached">Public databases</option>
|
|
|
33 <option value="history">Databases from your history</option>
|
|
|
34 </param>
|
|
|
35 <when value="cached">
|
|
|
36 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
|
|
|
37 <options from_data_table="qiime_taxonomy" />
|
|
|
38 </param>
|
|
|
39 </when>
|
|
|
40 <when value="history">
|
|
|
41 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
|
|
|
42 </when>
|
|
|
43 </conditional>
|
|
|
44
|
|
|
45 </inputs>
|
|
|
46 <outputs>
|
|
|
47 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
|
|
|
48 </outputs>
|
|
|
49 <help><![CDATA[
|
|
|
50 Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.
|
|
|
51 #######################################################################################
|
|
|
52
|
|
|
53 Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
|
|
|
54 for every inserted fragment. Then, look up the reference lineage string in
|
|
|
55 the reference taxonomy.
|
|
|
56
|
|
|
57 Parameters
|
|
|
58 ----------
|
|
|
59 representative_sequences : FeatureData[Sequence]
|
|
|
60 The sequences used for a 'sepp' run to produce the 'tree'.
|
|
|
61 tree : Phylogeny[Rooted]
|
|
|
62 The tree resulting from inserting fragments into a reference phylogeny,
|
|
|
63 i.e. the output of function 'sepp'
|
|
|
64 reference_taxonomy : FeatureData[Taxonomy], optional
|
|
|
65 Reference taxonomic table that maps every OTU-ID into a taxonomic
|
|
|
66 lineage string.
|
|
|
67
|
|
|
68 Returns
|
|
|
69 -------
|
|
|
70 classification : FeatureData[Taxonomy]
|
|
|
71 Taxonomic lineages for inserted fragments.
|
|
|
72 ]]></help>
|
|
|
73 <macros>
|
|
|
74 <import>qiime_citation.xml</import>
|
|
|
75 </macros>
|
|
|
76 <expand macro="qiime_citation"/>
|
|
|
77 </tool>
|
