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1 <tool id="Fetch Taxonomic Ranks" name="Fetch taxonomic representation" version="1.1.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package">taxonomy</requirement>
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5 </requirements>
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6 <command interpreter="python">gi2taxonomy.py $input $giField $idField $out_file1 ${GALAXY_DATA_INDEX_DIR}</command>
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7 <inputs>
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8 <param format="tabular" name="input" type="data" label="Show taxonomic representation for"></param>
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9 <param name="giField" label="GIs column" type="data_column" data_ref="input" numerical="True" help="select column containing GI numbers"/>
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10 <param name="idField" label="Name column" type="data_column" data_ref="input" help="select column containing identifiers you want to include into output"/>
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11 </inputs>
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12 <outputs>
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13 <data format="taxonomy" name="out_file1" />
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14 </outputs>
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15 <requirements>
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16 <requirement type="binary">taxBuilder</requirement>
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17 </requirements>
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18 <tests>
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19 <test>
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20 <param name="input" ftype="tabular" value="taxonomy2gi-input.tabular"/>
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21 <param name="giField" value="1"/>
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22 <param name="idField" value="2"/>
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23 <output name="out_file1" file="taxonomy2gi-output.tabular"/>
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24 </test>
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25 </tests>
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26
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27 <help>
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28
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29 .. class:: infomark
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30
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31 Use *Filter and Sort->Filter* to restrict output of this tool to desired taxonomic ranks. You can also use *Text Manipulation->Cut* to remove unwanted columns from the output.
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32
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33 ------
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34
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35 **What it does**
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36
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37 Fetches taxonomic information for a list of GI numbers (sequences identifiers used by the National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov).
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38
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39 -------
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40
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41 **Example**
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42
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43 Suppose you have BLAST output that looks like this::
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44
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45 +-----------------------+----------+----------+-----------------+------------+------+--------+
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46 | queryId | targetGI | identity | alignmentLength | mismatches | gaps | score |
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47 +-----------------------+----------+----------+-----------------+------------+------+--------+
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48 | 1L_EYKX4VC01BXWX1_265 | 1430919 | 90.09 | 212 | 15 | 6 | 252.00 |
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49 +-----------------------+----------+----------+-----------------+------------+------+--------+
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50
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51 and you want to obtain full taxonomic representation for GIs listed in *targetGI* column. If you set parameters as shown here:
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52
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53 .. image:: ./static/images/fetchTax.png
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54
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55
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56 the tool will generate the following output (you may need to scroll sideways to see the entire line)::
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57
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58 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
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59 1L_EYKX4VC01BXWX1_265 9606 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n 1430919
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60
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61 In other words the tool printed *Name column*, *taxonomy Id*, appended 22 columns containing taxonomic ranks from Superkingdom to Subspecies and added *GI* as the last column. Below is a formal definition of the output columns::
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62
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63 Column Definition
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64 ------- ------------------------------------------
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65 1 Name (specified by 'Name column' dropdown)
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66 2 GI (specified by 'GI column' dropdown)
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67 3 root
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68 4 superkingdom
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69 5 kingdom
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70 6 subkingdom
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71 7 superphylum
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72 8 phylum
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73 9 subphylum
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74 10 superclass
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75 11 class
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76 12 subclass
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77 13 superorder
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78 14 order
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79 15 suborder
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80 16 superfamily
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81 17 family
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82 18 subfamily
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83 19 tribe
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84 20 subtribe
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85 21 genus
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86 22 subgenus
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87 23 species
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88 24 subspecies
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89
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90 ------
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91
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92 .. class:: warningmark
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93
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94 **Why do I have these "n" things?**
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95
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96 Be aware that the NCBI taxonomy (ftp://ftp.ncbi.nih.gov/pub/taxonomy/) this tool relies upon is incomplete. This means that for many species one or more ranks are absent and represented as "**n**". In the above example *subkingdom*, *superphylum* etc. are missing.
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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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101
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102
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