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1 <tool id="find_diag_hits" name="Find diagnostic hits" version="1.0.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.0.0">taxonomy</requirement>
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5 </requirements>
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6 <command interpreter="python">find_diag_hits.py $input1 $id_col $rank_list $out_format $out_file1</command>
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7 <inputs>
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8 <param format="taxonomy" name="input1" type="data" label="Find diagnostic hits in"/>
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9 <param name="id_col" type="data_column" data_ref="input1" numerical="False" label="Select column with sequence id" />
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10 <param name="rank_list" type="select" display="checkboxes" multiple="true" label="select taxonomic ranks">
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11 <option value="superkingdom">Superkingdom</option>
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12 <option value="kingdom">Kingdom</option>
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13 <option value="subkingdom">Subkingdom</option>
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14 <option value="superphylum">Superphylum</option>
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15 <option value="phylum">Phylum</option>
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16 <option value="subphylum">Subphylum</option>
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17 <option value="superclass">Superclass</option>
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18 <option value="class">Class</option>
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19 <option value="subclass">Subclass</option>
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20 <option value="superorder">Superorder</option>
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21 <option value="order">Order</option>
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22 <option value="suborder">Suborder</option>
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23 <option value="superfamily">Superfamily</option>
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24 <option value="family">Family</option>
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25 <option value="subfamily">Subfamily</option>
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26 <option value="tribe">Tribe</option>
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27 <option value="subtribe">Subtribe</option>
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28 <option value="genus">Genus</option>
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29 <option value="subgenus">Subgenus</option>
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30 <option selected="true" value="species">Species</option>
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31 <option value="subspecies">Subspecies</option>
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32 </param>
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33 <param name="out_format" type="select" label="Select output format">
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34 <option value="reads">Diagnostic read list</option>
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35 <option value="counts">Number of diagnostic reads per taxonomic rank</option>
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36 </param>
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37 </inputs>
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38 <outputs>
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39 <data format="tabular" name="out_file1" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="input1" value="taxonomyGI.taxonomy" ftype="taxonomy"/>
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44 <param name="id_col" value="1" />
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45 <param name="rank_list" value="order,genus" />
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46 <param name="out_format" value="counts" />
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47 <output name="out_file1" file="find_diag_hits.tabular" />
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48 </test>
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49 </tests>
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50
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51
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52 <help>
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53
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54 **What it does**
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55
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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.
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57
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58 ------
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59
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60 **Example**
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61
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62 Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation::
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63
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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
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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
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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
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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
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68
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69 Running this tool with the following parameters:
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70
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71 * *Select column with sequence id* set to **c1**
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72 * *Select taxonomic ranks* with **order**, and **genus** checked
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73 * *Output format* set to **Diagnostic read list**
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74
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75 will return::
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76
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77 read2 Primates order
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78 read3 Primates order
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79 read2 Homo genus
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80 read3 Homo genus
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81
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82 Changing *Output format* set to **Number of diagnostic reads per taxonomic rank** will produce::
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83
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84 Primates 2 order
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85 Homo 2 genus
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86
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87 .. class:: infomark
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88
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89 Note that **read1** is omitted because it is non-unique: it hits Mammals and Insects at the same time.
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90
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91 --------
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92
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93 .. class:: warningmark
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94
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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.
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96
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97
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98 </help>
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99 </tool>
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