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1 <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8">
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2 <description>Convert BLAST XML output to tabular</description>
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3 <command interpreter="python">
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4 blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
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5 </command>
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6 <inputs>
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7 <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/>
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8 <param name="out_format" type="select" label="Output format">
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9 <option value="std" selected="True">Tabular (standard 12 columns)</option>
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10 <option value="ext">Tabular (extended 24 columns)</option>
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11 </param>
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12 </inputs>
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13 <outputs>
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14 <data name="tabular_file" format="tabular" label="BLAST results as tabular" />
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15 </outputs>
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16 <requirements>
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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="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
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21 <param name="out_format" value="std" />
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22 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar -->
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23 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" />
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24 </test>
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25 <test>
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26 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
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27 <param name="out_format" value="ext" />
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28 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar -->
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29 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" />
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30 </test>
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31 <test>
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32 <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" />
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33 <param name="out_format" value="std" />
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34 <!-- Note this has some white space differences from the actual blastp output -->
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35 <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" />
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36 </test>
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37 <test>
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38 <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
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39 <param name="out_format" value="std" />
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40 <!-- Note this has some white space differences from the actual blastx output -->
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41 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" />
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42 </test>
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43 <test>
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44 <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
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45 <param name="out_format" value="ext" />
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46 <!-- Note this has some white space and XXXX masking differences from the actual blastx output -->
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47 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" />
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48 </test>
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49 <test>
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50 <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" />
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51 <param name="out_format" value="std" />
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52 <!-- Note this has some white space differences from the actual blastx output -->
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53 <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" />
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54 </test>
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55 <test>
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56 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
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57 <param name="out_format" value="std" />
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58 <!-- Note this has some white space differences from the actual blastp output -->
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59 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" />
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60 </test>
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61 <test>
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62 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
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63 <param name="out_format" value="ext" />
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64 <!-- Note this has some white space differences from the actual blastp output -->
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65 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" />
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66 </test>
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67 </tests>
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68 <help>
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69
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70 **What it does**
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71
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72 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
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73 formats including tabular and a more detailed XML format. A complex workflow
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74 may need both the XML and the tabular output - but running BLAST twice is
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75 slow and wasteful.
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76
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77 This tool takes the BLAST XML output and by default converts it into the
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78 standard 12 column tabular equivalent:
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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 1 qseqid Query Seq-id (ID of your sequence)
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84 2 sseqid Subject Seq-id (ID of the database hit)
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85 3 pident Percentage of identical matches
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86 4 length Alignment length
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87 5 mismatch Number of mismatches
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88 6 gapopen Number of gap openings
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89 7 qstart Start of alignment in query
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90 8 qend End of alignment in query
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91 9 sstart Start of alignment in subject (database hit)
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92 10 send End of alignment in subject (database hit)
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93 11 evalue Expectation value (E-value)
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94 12 bitscore Bit score
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95 ====== ========= ============================================
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96
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97 The BLAST+ tools can optionally output additional columns of information,
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98 but this takes longer to calculate. Most (but not all) of these columns are
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99 included by selecting the extended tabular output. The extra columns are
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100 included *after* the standard 12 columns. This is so that you can write
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101 workflow filtering steps that accept either the 12 or 22 column tabular
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102 BLAST output.
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103
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104 ====== ============= ===========================================
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105 Column NCBI name Description
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106 ------ ------------- -------------------------------------------
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107 13 sallseqid All subject Seq-id(s), separated by a ';'
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108 14 score Raw score
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109 15 nident Number of identical matches
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110 16 positive Number of positive-scoring matches
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111 17 gaps Total number of gaps
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112 18 ppos Percentage of positive-scoring matches
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113 19 qframe Query frame
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114 20 sframe Subject frame
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115 21 qseq Aligned part of query sequence
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116 22 sseq Aligned part of subject sequence
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117 23 qlen Query sequence length
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118 24 slen Subject sequence length
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119 ====== ============= ===========================================
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120
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121 Beware that the XML file (and thus the conversion) and the tabular output
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122 direct from BLAST+ may differ in the presence of XXXX masking on regions
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123 low complexity (columns 21 and 22), and thus also calculated figures like
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124 the percentage idenity (column 3).
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125
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126 </help>
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127 </tool>
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