[2] | 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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