Mercurial > repos > bcclaywell > microbiome_pplacer_suite

comparison classification.xml @ 2:ce6db18f5fd3 draft

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author bcclaywell
date Thu, 26 Feb 2015 19:31:20 -0500
parents d4690e65afcd
children 3c50a937d7c1
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1:c8cc6529038c 2:ce6db18f5fd3
1 <tool id="PHYLO_classification" name="Output classifications" version="2.1.0">
2 <description>in tabular format</description>
3 <requirements>
4 <requirement type="package">yapp_env</requirement>
5 </requirements>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <version_command>echo "guppy $(guppy --version)"</version_command>
10 <command interpreter="bash">
11 classification-wrapper.sh ${config}
12 </command>
13 <stdio>
14 <expand macro="basic_errors"/>
15 </stdio>
16 <inputs>
17 <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/>
18 <param name="label_map" type="data" format="csv" label="Specimen-to-label map"/>
19 <param name="class_db" type="data" format="sqlite3" label="Placement database"/>
20 <param name="want_rank" type="select" label="Desired classification rank">
21 <option value="species" selected="true">Species</option>
22 <option value="genus">Genus</option>
23 <option value="family">Family</option>
24 <option value="order">Order</option>
25 <option value="class">Class</option>
26 <option value="phylum">Phylum</option>
27 </param>
28 </inputs>
29 <outputs>
30 <data name="by_taxon" format="csv" label="By-taxon classification"/>
31 <data name="by_specimen" format="csv" label="By-specimen classification"/>
32 <data name="tallies_wide" format="csv" label="Tallies-wide classification"/>
33 </outputs>
34 <configfiles>
35 <configfile name="config">
36 SPLIT_MAP="${split_map}"
37 LABEL_MAP="${label_map}"
38 CLASS_DB="${class_db}"
39 WANT_RANK="${want_rank}"
40
41 BY_TAXON="${by_taxon}"
42 BY_SPECIMEN="${by_specimen}"
43 TALLIES_WIDE="${tallies_wide}"
44 </configfile>
45 </configfiles>
46 <!-- The contents of the help tag is parsed as reStructuredText. Please see
47 help-template.rst for examples of commonly-used sections in other Galaxy
48 tools. -->
49 <help>
50
51 .. class:: infomark
52
53 **What it does**
54
55 This tool outputs the classifications made by ``pplacer`` to a tabular format
56 appropriate for use with R.
57
58 -----
59
60 **Example**
61
62 The classifications are simply done by containment. Say clade A of the
63 reference tree is the smallest such that contains a given placement. The most
64 specific classification for that read will be the lowest common ancestor of the
65 taxonomic classifications for the leaves of A. If the desired classification is
66 more specific than that, then we get a disconnect between the desired and the
67 actual classification. For example, if we try to classify at the species level
68 and the clade LCA is a genus, then we will get a genus name. If there is
69 uncertainty in read placement, then there is uncertainty in classification.
70
71 For example, here is a classification list made for one read using the tabular
72 output. The columns are as follows: read name, attempted rank for
73 classification, actual rank for classification, taxonomic identifier, and
74 confidence. You can see that in this example, there is some uncertainty at and
75 below species, but only one classification at the genus level::
76
77 GLKT0ZE01CQ2BU root root 1 1
78 GLKT0ZE01CQ2BU below_root below_root 131567 1
79 GLKT0ZE01CQ2BU superkingdom superkingdom 2 1
80 GLKT0ZE01CQ2BU below_superkingdom superkingdom 2 1
81 GLKT0ZE01CQ2BU below_below_superkingdom superkingdom 2 1
82 GLKT0ZE01CQ2BU superphylum superkingdom 2 1
83 GLKT0ZE01CQ2BU phylum phylum 1239 1
84 GLKT0ZE01CQ2BU subphylum phylum 1239 1
85 GLKT0ZE01CQ2BU class class 186801 1
86 GLKT0ZE01CQ2BU subclass class 186801 1
87 GLKT0ZE01CQ2BU order order 186802 1
88 GLKT0ZE01CQ2BU below_order order 186802 1
89 GLKT0ZE01CQ2BU below_below_order order 186802 1
90 GLKT0ZE01CQ2BU suborder order 186802 1
91 GLKT0ZE01CQ2BU family family 186804 1
92 GLKT0ZE01CQ2BU below_family family 186804 1
93 GLKT0ZE01CQ2BU genus genus 1257 1
94 GLKT0ZE01CQ2BU species_group genus 1257 1
95 GLKT0ZE01CQ2BU species_subgroup genus 1257 1
96 GLKT0ZE01CQ2BU species genus 1257 0.0732247
97 GLKT0ZE01CQ2BU species species 1261 0.853561
98 GLKT0ZE01CQ2BU species species 341694 0.073214
99 GLKT0ZE01CQ2BU below_species genus 1257 0.0732247
100 GLKT0ZE01CQ2BU below_species species 1261 0.853561
101 GLKT0ZE01CQ2BU below_species species 341694 0.073214
102
103 </help>
104 </tool>