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comparison tools/taxonomy/lca.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="lca1" name="Find lowest diagnostic rank" version="1.0.1">
2 <description></description>
3 <requirements>
4 <requirement type="package">taxonomy</requirement>
5 </requirements>
6 <command interpreter="python">
7 lca.py $input1 $out_file1 $rank_bound
8 </command>
9 <inputs>
10 <param format="taxonomy" name="input1" type="data" label="for taxonomy dataset"/>
11 <param name="rank_bound" label="require the lowest rank to be at least" type="select">
12 <option value="0">No restriction</option>
13 <option value="3">Superkingdom</option>
14 <option value="4">Kingdom</option>
15 <option value="5">Subkingdom</option>
16 <option value="6">Superphylum</option>
17 <option value="7">Phylum</option>
18 <option value="8">Subphylum</option>
19 <option value="9">Superclass</option>
20 <option value="10">Class</option>
21 <option value="11">Subclass</option>
22 <option value="12">Superorder</option>
23 <option value="13">Order</option>
24 <option value="14">Suborder</option>
25 <option value="15">Superfamily</option>
26 <option value="16">Family</option>
27 <option value="17">Subfamily</option>
28 <option value="18">Tribe</option>
29 <option value="19">Subtribe</option>
30 <option value="20">Genus</option>
31 <option value="21">Subgenus</option>
32 <option value="22">Species</option>
33 <option value="23">Subspecies</option>
34 </param>
35 </inputs>
36 <outputs>
37 <data format="taxonomy" name="out_file1" metadata_source="input1" />
38 </outputs>
39 <tests>
40 <test>
41 <param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/>
42 <param name="rank_bound" value="0" />
43 <output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/>
44 </test>
45 <test>
46 <param name="input1" value="lca_input2.taxonomy" ftype="taxonomy"/>
47 <param name="rank_bound" value="7" />
48 <output name="out_file1" file="lca_output2.taxonomy" ftype="taxonomy"/>
49 </test>
50
51 <!--Test case with invalid lines -->
52 <test>
53 <param name="input1" value="lca_input3.taxonomy" ftype="taxonomy"/>
54 <param name="rank_bound" value="10" />
55 <output name="out_file1" file="lca_output3.taxonomy" ftype="taxonomy"/>
56 </test>
57 </tests>
58
59 <help>
60
61 **What it does**
62
63 This tool identifies the lowest taxonomic rank for which a mategenomic sequencing read is diagnostic. It takes datasets produced by *Fetch Taxonomic Ranks* tool (aka Taxonomy format) as the input.
64
65 -------
66
67 **Example**
68
69 Suppose you have two reads, **read_1** and **read_2**, with the following taxonomic profiles (scroll sideways to see the entire dataset)::
70
71 read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1
72 read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 subgenus2 species2 subspecies2
73 read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum3 subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3
74 read_2 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4
75
76 For **read_1** taxonomic labels are consistent until the genus level, where the taxonomy splits into two branches, one ending with *subspecies1* and the other with *subspecies2*. This implies **that the lowest taxomomic rank read_1 can identify is SUBTRIBE**. Similarly, read_2 is diagnostic up until the **superphylum** level. As a results the output of this tool will be::
77
78 read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n
79 read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n n n n n n n n n n n n n n n n n
80
81 where, **n** means *EMPTY*.
82
83 --------
84
85 **What's up with the drop down?**
86
87 Why do we need the *require the lowest rank to be at least* dropdown? Let's look at the above example again. Suppose you need to find only those reads that are diagnostic on at least phylum level. To do this you need to set the *require the lowest rank to be at least* to **phylum**. As a result your output will look like this::
88
89 read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n
90
91 .. class:: infomark
92
93 Note, that **read_2** is now omitted as it matches two phyla (**phylum3** and **phylum4**) and therefore is not diagnostic (but rather cosmopolitan) on *phylum* level.
94
95
96
97
98
99 </help>
100 </tool>