comparison find_diag_hits.xml @ 0:acf51ff24c7d draft default tip

Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:25:21 -0500
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1 <tool id="find_diag_hits" name="Find diagnostic hits" version="1.0.0">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="1.0.0">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>