root/galaxy-central/tools/taxonomy/lca.xml

リビジョン 2, 5.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
63This 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
69Suppose 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
76For **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   
81where, **n** means *EMPTY*.
82
83--------
84
85**What's up with the drop down?**
86
87Why 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   
93Note, 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>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。