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1 <tool id="blast2go" name="Blast2GO" version="0.0.9">
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2 <description>Maps BLAST results to GO annotation terms</description>
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3 <requirements>
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4 <requirement type="package" version="2.5">b2g4pipe</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 blast2go.py "${xml}" "${prop.fields.path}" "${tab}"
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8 </command>
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9 <stdio>
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10 <!-- Wrapper ensures anything other than zero is an error -->
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11 <exit_code range="1:" />
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12 <exit_code range=":-1" />
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13 </stdio>
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14 <inputs>
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15 <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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16 <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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17 <options from_file="blast2go.loc">
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18 <column name="value" index="0"/>
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19 <column name="name" index="1"/>
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20 <column name="path" index="2"/>
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21 </options>
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data name="tab" format="tabular" label="Blast2GO ${prop.fields.name}" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="xml" value="blastp_sample.xml" ftype="blastxml"/>
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30 <param name="prop" value="Spain_2011_June"/>
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31 <output name="tab" file="blastp_sample.blast2go.tabular" ftype="tabular"/>
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32 </test>
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33 </tests>
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34 <help>
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35 .. class:: warningmark
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36
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37 **Note**. Blast2GO may take a substantial amount of time, especially if
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38 running against the public server in Spain. For large input datasets it
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39 is advisable to allow overnight processing, or consider subdividing.
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40
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41 -----
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42
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43 **What it does**
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44
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45 This runs b2g4Pipe v2.5, which is the command line (no GUI) version of
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46 Blast2GO designed for use in pipelines.
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47
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48 It takes as input BLAST XML results against a protein database, typically
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49 the NCBI non-redundant (NR) database. This tool will accept concatenated
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50 BLAST XML files (although they are technically invalid XML), which is very
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51 useful if you have sub-divided your protein FASTA files and run BLAST on
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52 them in batches.
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53
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54 The BLAST matches are used to assign Gene Ontology (GO) annotation terms
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55 to each query sequence.
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56
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57 The output from this tool is a tabular file containing three columns, with
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58 the order taken from query order in the original BLAST XML file:
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59
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60 ====== ====================
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61 Column Description
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62 ------ --------------------
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63 1 ID of query sequence
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64 2 GO term
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65 3 GO description
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66 ====== ====================
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67
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68 Note that if no GO terms are assigned to a sequence (e.g. if it had no
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69 BLAST matches), then it will not be present in the output file.
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70
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71 This tabular file is called an "Annotation File" in the Blast2GO GUI.
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72 If you download the tabular file, and rename it to use the extension
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73 ".annot", then it can be opened with the Blast2GO GUI via the "File",
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74 "Load Annotation (.annot)" menu (keyboard shortcut ALT+L). You can
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75 then run some of the interactive analyses offered in the GUI tool.
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76
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77
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78 **Advanced Settings**
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79
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80 Blast2GO has a properties setting file which includes which database
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81 server to connect to (e.g. the public server in Valencia, Spain, or a
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82 local server), as well as more advanced options such as thresholds and
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83 evidence code weights. To change these settings, your Galaxy administrator
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84 must create a new properties file, and add it to the drop down menu above.
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85
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86
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87 **References**
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88
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89 If you use this Galaxy tool in work leading to a scientific publication please
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90 cite the following papers:
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91
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92 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
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93 Galaxy tools and workflows for sequence analysis with applications
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94 in molecular plant pathology. PeerJ 1:e167
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95 http://dx.doi.org/10.7717/peerj.167
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96
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97 S. Götz et al. (2008).
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98 High-throughput functional annotation and data mining with the Blast2GO suite.
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99 Nucleic Acids Res. 36(10):3420–3435.
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100 http://dx.doi.org/10.1093/nar/gkn176
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101
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102 A. Conesa and S. Götz (2008).
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103 Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
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104 International Journal of Plant Genomics. 619832.
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105 http://dx.doi.org/10.1155/2008/619832
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106
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107 A. Conesa et al. (2005).
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108 Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
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109 Bioinformatics 21:3674-3676.
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110 http://dx.doi.org/10.1093/bioinformatics/bti610
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111
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112 See also http://www.blast2go.com/
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113
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114 This wrapper is available to install into other Galaxy Instances via the Galaxy
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115 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
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116
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117 </help>
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118 <citations>
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119 <citation type="doi">10.7717/peerj.167</citation>
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120 <citation type="doi">10.1093/nar/gkn176</citation>
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121 <citation type="doi">10.1155/2008/619832</citation>
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122 <citation type="doi">10.1093/bioinformatics/bti610</citation>
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123 </citations>
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124 </tool>
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