Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/blastxml_to_tabular.xml @ 10:70e7dcbf6573 draft
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
author | peterjc |
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date | Mon, 23 Sep 2013 06:14:13 -0400 |
parents | 1f546099212f |
children | 4c4a0da938ff |
rev | line source |
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10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
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1 <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.11"> |
3
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2 <description>Convert BLAST XML output to tabular</description> |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
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3 <version_command interpreter="python">blastxml_to_tabular.py --version</version_command> |
3
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4 <command interpreter="python"> |
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5 blastxml_to_tabular.py $blastxml_file $tabular_file $out_format |
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6 </command> |
8
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7 <stdio> |
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8 <!-- Anything other than zero is an error --> |
1f546099212f
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9 <exit_code range="1:" /> |
1f546099212f
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peterjc
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10 <exit_code range=":-1" /> |
1f546099212f
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11 </stdio> |
3
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12 <inputs> |
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13 <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> |
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14 <param name="out_format" type="select" label="Output format"> |
8
1f546099212f
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15 <option value="std">Tabular (standard 12 columns)</option> |
1f546099212f
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16 <option value="ext" selected="True">Tabular (extended 24 columns)</option> |
3
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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 as tabular" /> |
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21 </outputs> |
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22 <requirements> |
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23 </requirements> |
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24 <tests> |
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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="std" /> |
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28 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar --> |
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29 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.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_four_human_vs_rhodopsin.xml" ftype="blastxml" /> |
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33 <param name="out_format" value="ext" /> |
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34 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar --> |
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35 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.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="blastp_sample.xml" ftype="blastxml" /> |
643338ac83c0
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39 <param name="out_format" value="std" /> |
643338ac83c0
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40 <!-- Note this has some white space differences from the actual blastp output --> |
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41 <output name="tabular_file" file="blastp_sample_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="std" /> |
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46 <!-- Note this has some white space differences from the actual blastx output --> |
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47 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.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_rhodopsin_vs_four_human.xml" ftype="blastxml" /> |
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51 <param name="out_format" value="ext" /> |
643338ac83c0
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52 <!-- Note this has some white space and XXXX masking differences from the actual blastx output --> |
643338ac83c0
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53 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.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="blastx_sample.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 blastx output --> |
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59 <output name="tabular_file" file="blastx_sample_converted.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="std" /> |
643338ac83c0
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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_std.tabular" ftype="tabular" /> |
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66 </test> |
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67 <test> |
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68 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> |
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69 <param name="out_format" value="ext" /> |
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70 <!-- Note this has some white space differences from the actual blastp output --> |
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71 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" /> |
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72 </test> |
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73 </tests> |
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74 <help> |
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75 |
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76 **What it does** |
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77 |
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78 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of |
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79 formats including tabular and a more detailed XML format. A complex workflow |
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80 may need both the XML and the tabular output - but running BLAST twice is |
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81 slow and wasteful. |
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82 |
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83 This tool takes the BLAST XML output and can convert it into the |
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84 standard 12 column tabular equivalent: |
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85 |
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86 ====== ========= ============================================ |
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87 Column NCBI name Description |
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88 ------ --------- -------------------------------------------- |
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89 1 qseqid Query Seq-id (ID of your sequence) |
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90 2 sseqid Subject Seq-id (ID of the database hit) |
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91 3 pident Percentage of identical matches |
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92 4 length Alignment length |
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93 5 mismatch Number of mismatches |
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94 6 gapopen Number of gap openings |
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95 7 qstart Start of alignment in query |
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96 8 qend End of alignment in query |
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97 9 sstart Start of alignment in subject (database hit) |
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98 10 send End of alignment in subject (database hit) |
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99 11 evalue Expectation value (E-value) |
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100 12 bitscore Bit score |
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101 ====== ========= ============================================ |
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102 |
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103 The BLAST+ tools can optionally output additional columns of information, |
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104 but this takes longer to calculate. Most (but not all) of these columns are |
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105 included by selecting the extended tabular output. The extra columns are |
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106 included *after* the standard 12 columns. This is so that you can write |
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107 workflow filtering steps that accept either the 12 or 22 column tabular |
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108 BLAST output. This tool now uses this extended 24 column output by default. |
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109 |
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110 ====== ============= =========================================== |
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111 Column NCBI name Description |
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112 ------ ------------- ------------------------------------------- |
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113 13 sallseqid All subject Seq-id(s), separated by a ';' |
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114 14 score Raw score |
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115 15 nident Number of identical matches |
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116 16 positive Number of positive-scoring matches |
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117 17 gaps Total number of gaps |
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118 18 ppos Percentage of positive-scoring matches |
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119 19 qframe Query frame |
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120 20 sframe Subject frame |
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121 21 qseq Aligned part of query sequence |
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122 22 sseq Aligned part of subject sequence |
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123 23 qlen Query sequence length |
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124 24 slen Subject sequence length |
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125 ====== ============= =========================================== |
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126 |
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127 Beware that the XML file (and thus the conversion) and the tabular output |
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128 direct from BLAST+ may differ in the presence of XXXX masking on regions |
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129 low complexity (columns 21 and 22), and thus also calculated figures like |
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130 the percentage identity (column 3). |
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131 |
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132 **References** |
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133 |
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134 If you use this Galaxy tool in work leading to a scientific publication please |
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135 cite: |
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136 |
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137 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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138 Galaxy tools and workflows for sequence analysis with applications |
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139 in molecular plant pathology. PeerJ 1:e167 |
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140 http://dx.doi.org/10.7717/peerj.167 |
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141 |
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142 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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143 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
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144 </help> |
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145 </tool> |