|
0
|
1 <tool id="find_diag_hits" name="Find diagnostic hits" version="1.0.0">
|
|
|
2 <description></description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package">taxonomy</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command interpreter="python">find_diag_hits.py $input1 $id_col $rank_list $out_format $out_file1</command>
|
|
|
7 <inputs>
|
|
|
8 <param format="taxonomy" name="input1" type="data" label="Find diagnostic hits in"/>
|
|
|
9 <param name="id_col" type="data_column" data_ref="input1" numerical="False" label="Select column with sequence id" />
|
|
|
10 <param name="rank_list" type="select" display="checkboxes" multiple="true" label="select taxonomic ranks">
|
|
|
11 <option value="superkingdom">Superkingdom</option>
|
|
|
12 <option value="kingdom">Kingdom</option>
|
|
|
13 <option value="subkingdom">Subkingdom</option>
|
|
|
14 <option value="superphylum">Superphylum</option>
|
|
|
15 <option value="phylum">Phylum</option>
|
|
|
16 <option value="subphylum">Subphylum</option>
|
|
|
17 <option value="superclass">Superclass</option>
|
|
|
18 <option value="class">Class</option>
|
|
|
19 <option value="subclass">Subclass</option>
|
|
|
20 <option value="superorder">Superorder</option>
|
|
|
21 <option value="order">Order</option>
|
|
|
22 <option value="suborder">Suborder</option>
|
|
|
23 <option value="superfamily">Superfamily</option>
|
|
|
24 <option value="family">Family</option>
|
|
|
25 <option value="subfamily">Subfamily</option>
|
|
|
26 <option value="tribe">Tribe</option>
|
|
|
27 <option value="subtribe">Subtribe</option>
|
|
|
28 <option value="genus">Genus</option>
|
|
|
29 <option value="subgenus">Subgenus</option>
|
|
|
30 <option selected="true" value="species">Species</option>
|
|
|
31 <option value="subspecies">Subspecies</option>
|
|
|
32 </param>
|
|
|
33 <param name="out_format" type="select" label="Select output format">
|
|
|
34 <option value="reads">Diagnostic read list</option>
|
|
|
35 <option value="counts">Number of diagnostic reads per taxonomic rank</option>
|
|
|
36 </param>
|
|
|
37 </inputs>
|
|
|
38 <outputs>
|
|
|
39 <data format="tabular" name="out_file1" />
|
|
|
40 </outputs>
|
|
|
41 <tests>
|
|
|
42 <test>
|
|
|
43 <param name="input1" value="taxonomyGI.taxonomy" ftype="taxonomy"/>
|
|
|
44 <param name="id_col" value="1" />
|
|
|
45 <param name="rank_list" value="order,genus" />
|
|
|
46 <param name="out_format" value="counts" />
|
|
|
47 <output name="out_file1" file="find_diag_hits.tabular" />
|
|
|
48 </test>
|
|
|
49 </tests>
|
|
|
50
|
|
|
51
|
|
|
52 <help>
|
|
|
53
|
|
|
54 **What it does**
|
|
|
55
|
|
|
56 When performing metagenomic analyses it is often necessary to identify sequence reads corresponding to a particular taxonomic group, or, in other words, diagnostic of a particular taxonomic rank. This utility performs this analysis. It takes data generated by *Taxonomy manipulation->Fetch Taxonomic Ranks* as input and outputs either a list of sequence reads unique to a particular taxonomic rank, or a list of taxonomic ranks and the count of unique reads corresponding to each rank.
|
|
|
57
|
|
|
58 ------
|
|
|
59
|
|
|
60 **Example**
|
|
|
61
|
|
|
62 Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation::
|
|
|
63
|
|
|
64 read1 2 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n
|
|
|
65 read2 12585 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n
|
|
|
66 read1 58615 root Eukaryota Metazoa n n Arthropoda n Hexapoda Insecta Neoptera Amphiesmenoptera Lepidoptera Glossata Papilionoidea Nymphalidae Nymphalinae Melitaeini Phyciodina Anthanassa n Anthanassa otanes n
|
|
|
67 read3 56785 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n
|
|
|
68
|
|
|
69 Running this tool with the following parameters:
|
|
|
70
|
|
|
71 * *Select column with sequence id* set to **c1**
|
|
|
72 * *Select taxonomic ranks* with **order**, and **genus** checked
|
|
|
73 * *Output format* set to **Diagnostic read list**
|
|
|
74
|
|
|
75 will return::
|
|
|
76
|
|
|
77 read2 Primates order
|
|
|
78 read3 Primates order
|
|
|
79 read2 Homo genus
|
|
|
80 read3 Homo genus
|
|
|
81
|
|
|
82 Changing *Output format* set to **Number of diagnostic reads per taxonomic rank** will produce::
|
|
|
83
|
|
|
84 Primates 2 order
|
|
|
85 Homo 2 genus
|
|
|
86
|
|
|
87 .. class:: infomark
|
|
|
88
|
|
|
89 Note that **read1** is omitted because it is non-unique: it hits Mammals and Insects at the same time.
|
|
|
90
|
|
|
91 --------
|
|
|
92
|
|
|
93 .. class:: warningmark
|
|
|
94
|
|
|
95 This tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* contains the order name (Primates) while *Bos taurus* does not.
|
|
|
96
|
|
|
97
|
|
|
98 </help>
|
|
|
99 </tool>
|
