Mercurial > repos > dfornika > blast_xml_to_tabular

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planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 3ee146d311de3deb2008d6690d8f2c9a05025d6d-dirty
author dfornika
date Wed, 11 Sep 2019 22:06:49 -0400
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efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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1 <tool id="blast_xml_to_tabular" name="BLAST XML to tabular" version="1.1.0">
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2 <description>Convert BLAST XML output to tabular</description>
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3 <command detect_errors="exit_code">
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4 <![CDATA[
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5 '$__tool_directory__/blast_xml_to_tabular.py'
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6 '${blastxml_file}'
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7 '${tabular_file}'
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8 '${out_format}'
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9 ]]>
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10 </command>
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11 <inputs>
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12 <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/>
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13 <param name="out_format" type="select" label="Output format">
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14 <option value="std" selected="True">Tabular (standard 12 columns)</option>
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15 <option value="ext">Tabular (extended 24 columns)</option>
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16 <option value="ext+">Tabular (extended 26 columns)</option>
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17 </param>
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18 </inputs>
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19 <outputs>
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20 <data name="tabular_file" format="tabular" label="BLAST results: data $blastxml_file.hid as tabular" />
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21 </outputs>
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22 <help>
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23
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24 .. class:: infomark
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25
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26 **What it does**
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27
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28 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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29 formats including tabular and a more detailed XML format. A complex workflow
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30 may need both the XML and the tabular output - but running BLAST twice is
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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31 slow and wasteful.
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32
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33 This tool takes the BLAST XML output and by default converts it into the
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34 standard 12 column tabular equivalent:
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35
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36 ====== ========= ============================================
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37 Column NCBI name Description
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38 ------ --------- --------------------------------------------
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39 1 qseqid Query Seq-id (ID of your sequence)
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40 2 sseqid Subject Seq-id (ID of the database hit)
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41 3 pident Percentage of identical matches
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42 4 length Alignment length
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43 5 mismatch Number of mismatches
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44 6 gapopen Number of gap openings
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45 7 qstart Start of alignment in query
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46 8 qend End of alignment in query
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47 9 sstart Start of alignment in subject (database hit)
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48 10 send End of alignment in subject (database hit)
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49 11 evalue Expectation value (E-value)
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50 12 bitscore Bit score
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51 ====== ========= ============================================
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52
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53 The BLAST+ tools can optionally output additional columns of information,
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54 but this takes longer to calculate. Most (but not all) of these columns are
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55 included by selecting the extended tabular output. The extra columns are
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56 included *after* the standard 12 columns. This is so that you can write
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57 workflow filtering steps that accept either the 12 or 24 column tabular
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58 BLAST output.
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59
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60 ====== ============= ===========================================
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61 Column NCBI name Description
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62 ------ ------------- -------------------------------------------
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63 13 sallseqid All subject Seq-id(s), separated by a ';'
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64 14 score Raw score
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65 15 nident Number of identical matches
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66 16 positive Number of positive-scoring matches
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67 17 gaps Total number of gaps
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68 18 ppos Percentage of positive-scoring matches
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69 19 qframe Query frame
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70 20 sframe Subject frame
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71 21 qseq Aligned part of query sequence
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72 22 sseq Aligned part of subject sequence
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73 23 qlen Query sequence length
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74 24 slen Subject sequence length
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75 ====== ============= ===========================================
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76
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77 Very slight modifications were made to the "BLAST XML to tabular" tool that
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78 ships with Galaxy to output two more column columns:
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79
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80 ====== ============= ===========================================
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81 Column NCBI name Description
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82 ------ ------------- -------------------------------------------
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83 25 pcov Percentage coverage
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84 26 sallseqdescr All subject Seq-descr(s), separated by a ','
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85 ====== ============= ===========================================
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86
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87 ----
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88
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89 .. class:: infomark
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90
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91 This is a slightly modified version of a tool that ships with Galaxy.
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92 If the 12 or 24 columns formats are desired, use the original tool.
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93
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94 .. class:: warningmark
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95
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96 Beware that the XML file (and thus the conversion) and the tabular output
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97 direct from BLAST+ may differ in the presence of XXXX masking on regions
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98 low complexity (columns 21 and 22), and thus also calculated figures like
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99 the percentage identity (column 3).
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100
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101 </help>
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102 </tool>