Mercurial > repos > peterjc > blastxml_to_top_descr
annotate tools/blastxml_to_top_descr/blastxml_to_top_descr.xml @ 11:98f8431dab44 draft
Uploaded v0.1.0, now also handles extended tabular BLAST output.
author | peterjc |
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date | Fri, 13 Jun 2014 07:07:35 -0400 |
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children | fe1ed74793c9 |
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1 <tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.0"> |
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2 <description>Make a table from BLAST output</description> |
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3 <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> |
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4 <command interpreter="python"> |
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5 blastxml_to_top_descr.py |
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6 -f "$input.in_format" |
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7 #if $input.in_format == "tabular": |
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8 --qseqid $input.qseqid |
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9 --sseqid $input.sseqid |
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10 --salltitles $input.salltitles |
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11 #end if |
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12 -o "${tabular_file}" |
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13 -t ${topN} |
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14 "${in_file}" |
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15 </command> |
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16 <stdio> |
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17 <!-- Assume anything other than zero is an error --> |
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18 <exit_code range="1:" /> |
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19 <exit_code range=":-1" /> |
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20 </stdio> |
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21 <inputs> |
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22 <conditional name="input"> |
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23 <param name="in_format" type="select" label="Input format"> |
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24 <option value="blastxml" select="True">BLAST XML</option> |
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25 <option value="tabular">Tabular</option> |
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26 </param> |
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27 <when value="blastxml"> |
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28 <param name="in_file" type="data" format="blastxml" label="BLAST results as XML"/> |
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29 </when> |
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30 <when value="tabular"> |
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31 <param name="in_file" type="data" format="tabular" label="BLAST results as tabular"/> |
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32 <param name="qseqid" type="data_column" data_ref="in_file" |
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33 multiple="False" numerical="False" default_value="1" value="1" |
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34 label="Column containing query ID (qseqid)" |
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35 help="This is column 1 in standard BLAST tabular output" /> |
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36 <param name="sseqid" type="data_column" data_ref="in_file" |
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37 multiple="False" numerical="False" default_value="2" value="2" |
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38 label="Column containing match ID (sseqid)" |
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39 help="This is column 2 in standard BLAST tabular output"/> |
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40 <param name="salltitles" type="data_column" data_ref="in_file" |
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41 multiple="False" numerical="False" default_value="25" value="25" |
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42 label="Column containing containing descriptions (salltitles)" |
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43 help="This is column 25 in the default extended BLAST tabular output"/> |
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44 </when> |
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45 </conditional> |
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46 <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/> |
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47 </inputs> |
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48 <outputs> |
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49 <data name="tabular_file" format="tabular" label="Top $topN descriptions from $input.in_file.name" /> |
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50 </outputs> |
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51 <requirements> |
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52 </requirements> |
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53 <tests> |
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54 <test> |
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55 <param name="in_format" value="blastxml" /> |
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56 <param name="in_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> |
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57 <param name="topN" value="3" /> |
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58 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3.tabular" ftype="tabular" /> |
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59 </test> |
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60 <test> |
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61 <param name="in_format" value="tabular" /> |
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62 <param name="in_file" value="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" /> |
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63 <param name="topN" value="3" /> |
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64 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3_positive.tabular" ftype="tabular" /> |
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65 </test> |
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66 </tests> |
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67 <help> |
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68 |
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69 **What it does** |
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70 |
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71 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of |
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72 formats including text, tabular and a more detailed XML format. You can |
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73 do a lot of things with tabular files in Galaxy (sorting, filtering, joins, |
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74 etc), however until BLAST+ 2.2.28 the tabular output never included the |
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75 hit descriptions (titles) found in the other output formats. |
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76 |
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77 This tool turns a BLAST XML file into a simple tabular file containing |
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78 one row per query sequence, containing the query identifier and then |
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79 the three (by default) top hit descriptions (i.e. the first three). If |
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80 a query doesn't have that many hits, then these entries are left blank. |
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81 |
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82 This tool can also be used with the tabular output from BLAST+ instead, |
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83 provided the relevant columns are provided. The default settings will |
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84 work with the default 25 column extended output from the BLAST+ tools |
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85 wrapped in Galaxy. Note if a query has *no* hits, it does not appear in |
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86 the BLAST tabular output. |
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87 |
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88 **Example Usage** |
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89 |
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90 One simple usage would be to take a transcriptome assembly or set of |
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91 gene predictions, run a BLAST search against the NCBI NR database, and |
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92 then use this tool to make a table of the top three BLAST hits. This |
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93 can give you a 'quick and dirty' crude annotation, potentially enough |
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94 to spot some problems (e.g. bacterial contaimination could be very |
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95 obvious). |
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96 |
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97 **References** |
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98 |
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99 If you use this Galaxy tool in work leading to a scientific publication please |
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100 cite: |
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101 |
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102 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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103 Galaxy tools and workflows for sequence analysis with applications |
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104 in molecular plant pathology. PeerJ 1:e167 |
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105 http://dx.doi.org/10.7717/peerj.167 |
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106 |
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107 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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108 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr |
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109 |
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110 </help> |
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111 </tool> |