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1 <tool id="lca1" name="Find lowest diagnostic rank" version="1.0.1">
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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">
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7 lca.py $input1 $out_file1 $rank_bound
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8 </command>
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9 <inputs>
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10 <param format="taxonomy" name="input1" type="data" label="for taxonomy dataset"/>
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11 <param name="rank_bound" label="require the lowest rank to be at least" type="select">
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12 <option value="0">No restriction</option>
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13 <option value="3">Superkingdom</option>
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14 <option value="4">Kingdom</option>
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15 <option value="5">Subkingdom</option>
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16 <option value="6">Superphylum</option>
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17 <option value="7">Phylum</option>
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18 <option value="8">Subphylum</option>
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19 <option value="9">Superclass</option>
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20 <option value="10">Class</option>
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21 <option value="11">Subclass</option>
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22 <option value="12">Superorder</option>
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23 <option value="13">Order</option>
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24 <option value="14">Suborder</option>
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25 <option value="15">Superfamily</option>
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26 <option value="16">Family</option>
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27 <option value="17">Subfamily</option>
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28 <option value="18">Tribe</option>
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29 <option value="19">Subtribe</option>
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30 <option value="20">Genus</option>
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31 <option value="21">Subgenus</option>
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32 <option value="22">Species</option>
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33 <option value="23">Subspecies</option>
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data format="taxonomy" name="out_file1" metadata_source="input1" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/>
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42 <param name="rank_bound" value="0" />
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43 <output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/>
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44 </test>
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45 <test>
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46 <param name="input1" value="lca_input2.taxonomy" ftype="taxonomy"/>
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47 <param name="rank_bound" value="7" />
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48 <output name="out_file1" file="lca_output2.taxonomy" ftype="taxonomy"/>
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49 </test>
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50
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51 <!--Test case with invalid lines -->
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52 <test>
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53 <param name="input1" value="lca_input3.taxonomy" ftype="taxonomy"/>
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54 <param name="rank_bound" value="10" />
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55 <output name="out_file1" file="lca_output3.taxonomy" ftype="taxonomy"/>
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56 </test>
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57 </tests>
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58
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59 <help>
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60
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61 **What it does**
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62
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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.
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64
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65 -------
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66
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67 **Example**
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68
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69 Suppose you have two reads, **read_1** and **read_2**, with the following taxonomic profiles (scroll sideways to see the entire dataset)::
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70
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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
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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
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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
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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
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75
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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::
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77
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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
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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
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80
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81 where, **n** means *EMPTY*.
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82
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83 --------
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84
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85 **What's up with the drop down?**
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86
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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::
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88
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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
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90
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91 .. class:: infomark
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92
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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.
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94
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95
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96
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97
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98
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99 </help>
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100 </tool>
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