annotate qiime2/qiime_fragment-insertion_classify-otus-experimental.xml @ 0:370e0b6e9826 draft

Uploaded
author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
parents
children f190567fe3f6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime fragment-insertion classify-otus-experimental
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-representative-sequences=$irepresentativesequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-tree=$itree --o-classification=oclassification
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 #if str( $id_to_taxonomy_fp.selector ) == 'history'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 --i-reference-taxonomy '$tax'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #else:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 --i-reference-taxonomy '$tax'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 cp oclassification.qza $oclassification
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 <conditional name="id_to_taxonomy_fp" optional="True">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 <param name="selector" type="select" label="Reference taxonomy to query">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 <option value="cached">Public databases</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 <option value="history">Databases from your history</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 <when value="cached">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 <options from_data_table="qiime_taxonomy" />
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 </when>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 <when value="history">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 </when>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 </conditional>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 #######################################################################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 for every inserted fragment. Then, look up the reference lineage string in
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 the reference taxonomy.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 representative_sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 The sequences used for a 'sepp' run to produce the 'tree'.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 tree : Phylogeny[Rooted]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 The tree resulting from inserting fragments into a reference phylogeny,
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 i.e. the output of function 'sepp'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 reference_taxonomy : FeatureData[Taxonomy], optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 Reference taxonomic table that maps every OTU-ID into a taxonomic
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 lineage string.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 classification : FeatureData[Taxonomy]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 Taxonomic lineages for inserted fragments.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 </tool>