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annotate tools/ncbi_blast_plus/blast2go.xml @ 1:0f159cf346c8

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Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 16:29:28 -0400
parents cd52c931b325
children e88a3246520e
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0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
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1 <tool id="blast2go" name="Blast2GO" version="0.0.2">
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2 <description>Maps BLAST results to GO annotation terms</description>
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3 <command interpreter="python">
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4 blast2go.py $xml ${prop.fields.path} $tab
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5 </command>
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6 <inputs>
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7 <param name="xml" type="data" format="blastxml" label="BLAST XML results" description="You must have run BLAST against a protein database such as the NCBI non-redundant (NR) database. Use BLASTX for nucleotide queries, BLASTP for protein queries." />
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8 <param name="prop" type="select" label="Blast2GO settings" description="One or more configurations can be setup, such as using the Blast2GO team's server in Spain, or a local database.">
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9 <options from_file="blast2go.loc">
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10 <column name="value" index="0"/>
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11 <column name="name" index="1"/>
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12 <column name="path" index="2"/>
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13 </options>
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14 </param>
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15 </inputs>
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16 <outputs>
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17 <data name="tab" format="tabular" label="Blast2GO ${prop.fields.name}" />
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18 </outputs>
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19 <requirements>
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20 </requirements>
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21 <tests>
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22 </tests>
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23 <help>
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24 .. class:: warningmark
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25
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26 **Note**. Blast2GO may take a substantial amount of time, especially if
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27 running against the public server in Spain. For large input datasets it
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28 is advisable to allow overnight processing, or consider subdividing.
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29
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30 -----
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31
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32 **What it does**
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33
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34 This runs b2g4Pipe, the command line (no GUI) version of Blast2GO designed
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35 for use in pipelines.
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36
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37 It takes as input BLAST XML results against a protein database, typically
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38 the NCBI non-redundant (NR) database. This tool will accept concatenated
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39 BLAST XML files (although they are technically invalid XML), which is very
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40 useful if you have sub-divided your protein FASTA files and run BLAST on
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41 them in batches.
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42
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43 The BLAST matches are used to assign Gene Ontology (GO) annotation terms
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44 to each query sequence.
0
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45
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46 The output from this tool is a tabular file containing three columns, with
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47 the order taken from query order in the original BLAST XML file:
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48
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49 ====== ====================================
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50 Column Description
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51 ------ ------------------------------------
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52 1 ID and description of query sequence
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53 2 GO term
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54 3 GO description
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55 ====== ====================================
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56
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57 Note that if no GO terms are assigned to a sequence (e.g. if it had no
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58 BLAST matches), then it will not be present in the output file.
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59
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60
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61 **Advanced Settings**
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62
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63 Blast2GO has a properties setting file which includes which database
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64 server to connect to (e.g. the public server in Valencia, Spain, or a
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65 local server), as well as more advanced options such as thresholds and
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66 evidence code weights. To change these settings, your Galaxy administrator
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67 must create a new properties file, and add it to the drop down menu above.
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69
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70 **References**
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71
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72 S. Götz et al.
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73 High-throughput functional annotation and data mining with the Blast2GO suite.
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74 Nucleic Acids Res. 36(10):3420–3435, 2008.
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75 http://dx.doi.org/10.1093/nar/gkn176
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76
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77 A. Conesa and S. Götz.
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78 Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
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79 Int. J. Plant Genomics. 619832, 2008.
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80 http://dx.doi.org/10.1155/2008/619832
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81
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82 A. Conesa et al.
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83 Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
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84 Bioinformatics 21:3674-3676, 2005.
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85 http://dx.doi.org/10.1093/bioinformatics/bti610
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86
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87 http://www.blast2go.org/
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88
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89 </help>
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90 </tool>