Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/blastxml_to_tabular.xml @ 22:6f386c5dc4fb draft
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
author | peterjc |
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date | Mon, 18 Sep 2017 06:21:27 -0400 |
parents | 7f3c448e119b |
children | 31e517610e1f |
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17
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v0.1.05 - Update citation information now GigaScience paper is out
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1 <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@WRAPPER_VERSION@"> |
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2 <description>Convert BLAST XML output to tabular</description> |
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3 <macros> |
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4 <import>ncbi_macros.xml</import> |
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5 </macros> |
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6 <version_command>python $__tool_directory__/blastxml_to_tabular.py --version</version_command> |
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7 <command detect_errors="aggressive"> |
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8 python $__tool_directory__/blastxml_to_tabular.py -o '$tabular_file' |
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9 #if $output.out_format == "cols": |
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10 #set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", " ").replace(",,", ",").replace(",", " ") |
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11 -c '$cols' |
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12 #else |
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13 -c '$output.out_format' |
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14 #end if |
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15 #for i in $blastxml_file#'${i}' #end for# |
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16 </command> |
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17 <inputs> |
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18 <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/> |
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19 <conditional name="output"> |
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20 <param name="out_format" type="select" label="Output format"> |
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21 <option value="std" selected="true">Tabular (standard 12 columns)</option> |
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22 <option value="ext">Tabular (extended 25 columns)</option> |
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23 <option value="cols">Tabular (select columns to output)</option> |
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24 </param> |
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25 <when value="std"/> |
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peterjc
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26 <when value="ext"/> |
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27 <when value="cols"> |
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28 <param name="std_cols" type="select" multiple="true" display="checkboxes" label="Standard columns"> |
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29 <option selected="true" value="qseqid">qseqid = Query Seq-id (ID of your sequence)</option> |
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30 <option selected="true" value="sseqid">sseqid = Subject Seq-id (ID of the database hit)</option> |
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31 <option selected="true" value="pident">pident = Percentage of identical matches</option> |
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32 <option selected="true" value="length">length = Alignment length</option> |
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33 <option selected="true" value="mismatch">mismatch = Number of mismatches</option> |
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34 <option selected="true" value="gapopen">gapopen = Number of gap openings</option> |
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35 <option selected="true" value="qstart">qstart = Start of alignment in query</option> |
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36 <option selected="true" value="qend">qend = End of alignment in query</option> |
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37 <option selected="true" value="sstart">sstart = Start of alignment in subject (database hit)</option> |
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38 <option selected="true" value="send">send = End of alignment in subject (database hit)</option> |
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39 <option selected="true" value="evalue">evalue = Expectation value (E-value)</option> |
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40 <option selected="true" value="bitscore">bitscore = Bit score</option> |
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41 </param> |
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42 <param name="ext_cols" type="select" multiple="true" display="checkboxes" label="Extended columns"> |
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43 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option> |
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44 <option value="score">score = Raw score</option> |
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45 <option value="nident">nident = Number of identical matches</option> |
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46 <option value="positive">positive = Number of positive-scoring matches</option> |
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47 <option value="gaps">gaps = Total number of gaps</option> |
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48 <option value="ppos">ppos = Percentage of positive-scoring matches</option> |
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49 <option value="qframe">qframe = Query frame</option> |
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50 <option value="sframe">sframe = Subject frame</option> |
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51 <option value="qseq">qseq = Aligned part of query sequence</option> |
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52 <option value="sseq">sseq = Aligned part of subject sequence</option> |
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53 <option value="qlen">qlen = Query sequence length</option> |
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54 <option value="slen">slen = Subject sequence length</option> |
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55 <option value="salltitles">salltitles = All subject title(s), separated by a '<>'</option> |
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56 </param> |
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57 </when> |
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58 </conditional> |
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59 </inputs> |
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60 <outputs> |
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61 <data name="tabular_file" format="tabular" label="$on_string (as tabular)" /> |
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62 </outputs> |
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63 <tests> |
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64 <test> |
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65 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> |
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66 <param name="out_format" value="std" /> |
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67 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar --> |
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68 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" /> |
643338ac83c0
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69 </test> |
643338ac83c0
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peterjc
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70 <test> |
643338ac83c0
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71 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> |
643338ac83c0
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peterjc
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72 <param name="out_format" value="ext" /> |
643338ac83c0
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73 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar --> |
643338ac83c0
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74 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" /> |
643338ac83c0
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peterjc
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75 </test> |
643338ac83c0
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peterjc
parents:
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76 <test> |
643338ac83c0
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77 <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" /> |
643338ac83c0
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peterjc
parents:
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78 <param name="out_format" value="std" /> |
643338ac83c0
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peterjc
parents:
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79 <!-- Note this has some white space differences from the actual blastp output --> |
643338ac83c0
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peterjc
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80 <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" /> |
643338ac83c0
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peterjc
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81 </test> |
643338ac83c0
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peterjc
parents:
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82 <test> |
643338ac83c0
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peterjc
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83 <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> |
643338ac83c0
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peterjc
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84 <param name="out_format" value="std" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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85 <!-- Note this has some white space differences from the actual blastx output --> |
643338ac83c0
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peterjc
parents:
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86 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" /> |
643338ac83c0
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peterjc
parents:
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87 </test> |
643338ac83c0
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peterjc
parents:
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88 <test> |
643338ac83c0
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peterjc
parents:
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89 <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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90 <param name="out_format" value="ext" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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91 <!-- Note this has some white space and XXXX masking differences from the actual blastx output --> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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92 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" /> |
643338ac83c0
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peterjc
parents:
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93 </test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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94 <test> |
643338ac83c0
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peterjc
parents:
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95 <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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|
96 <param name="out_format" value="std" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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|
97 <!-- Note this has some white space differences from the actual blastx output --> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
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98 <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" /> |
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99 </test> |
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100 <test> |
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101 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> |
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102 <param name="out_format" value="std" /> |
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103 <!-- Note this has some white space differences from the actual blastp output --> |
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104 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" /> |
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105 </test> |
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106 <test> |
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107 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> |
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108 <param name="out_format" value="ext" /> |
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109 <!-- Note this has some white space differences from the actual blastp output --> |
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110 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" /> |
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111 </test> |
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112 <test> |
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113 <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> |
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114 <param name="out_format" value="std" /> |
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115 <output name="tabular_file" file="blastn_arabidopsis.standard.tabular" ftype="tabular" /> |
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116 </test> |
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117 <test> |
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118 <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> |
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119 <param name="out_format" value="ext" /> |
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120 <output name="tabular_file" file="blastn_arabidopsis.extended.tabular" ftype="tabular" /> |
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121 </test> |
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122 <!-- there are some harmless white space differences in our conversion to the BLAST+ output here: --> |
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123 <test> |
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124 <param name="blastxml_file" value="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> |
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125 <param name="out_format" value="std" /> |
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126 <output name="tabular_file" file="blastn_rhodopsin_vs_three_human_converted.tabular" ftype="tabular" /> |
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127 </test> |
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128 <test> |
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129 <param name="blastxml_file" value="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> |
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130 <param name="out_format" value="cols" /> |
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131 <param name="std_cols" value="qseqid,sseqid,pident" /> |
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132 <param name="ext_cols" value="qlen,slen" /> |
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133 <output name="tabular_file" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> |
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134 </test> |
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135 </tests> |
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136 <help> |
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137 |
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138 **What it does** |
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139 |
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140 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of |
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141 formats including tabular and a more detailed XML format. A complex workflow |
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142 may need both the XML and the tabular output - but running BLAST twice is |
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143 slow and wasteful. |
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144 |
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145 This tool takes the BLAST XML output and can convert it into the |
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146 standard 12 column tabular equivalent: |
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147 |
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148 ====== ========= ============================================ |
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149 Column NCBI name Description |
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150 ------ --------- -------------------------------------------- |
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151 1 qseqid Query Seq-id (ID of your sequence) |
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152 2 sseqid Subject Seq-id (ID of the database hit) |
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153 3 pident Percentage of identical matches |
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154 4 length Alignment length |
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155 5 mismatch Number of mismatches |
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156 6 gapopen Number of gap openings |
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157 7 qstart Start of alignment in query |
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158 8 qend End of alignment in query |
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159 9 sstart Start of alignment in subject (database hit) |
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160 10 send End of alignment in subject (database hit) |
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161 11 evalue Expectation value (E-value) |
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162 12 bitscore Bit score |
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163 ====== ========= ============================================ |
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164 |
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165 The BLAST+ tools can optionally output additional columns of information, |
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166 but this takes longer to calculate. Most (but not all) of these columns are |
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167 included by selecting the extended tabular output. The extra columns are |
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168 included *after* the standard 12 columns. This is so that you can write |
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169 workflow filtering steps that accept either the 12 or 25 column tabular |
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170 BLAST output. This tool now uses this extended 25 column output by default. |
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171 |
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172 ====== ============= =========================================== |
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173 Column NCBI name Description |
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174 ------ ------------- ------------------------------------------- |
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175 13 sallseqid All subject Seq-id(s), separated by a ';' |
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176 14 score Raw score |
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177 15 nident Number of identical matches |
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178 16 positive Number of positive-scoring matches |
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179 17 gaps Total number of gaps |
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180 18 ppos Percentage of positive-scoring matches |
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181 19 qframe Query frame |
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182 20 sframe Subject frame |
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183 21 qseq Aligned part of query sequence |
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184 22 sseq Aligned part of subject sequence |
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185 23 qlen Query sequence length |
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186 24 slen Subject sequence length |
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187 25 salltitles All subject title(s), separated by a '<>' |
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188 ====== ============= =========================================== |
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189 |
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190 Beware that the XML file (and thus the conversion) and the tabular output |
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191 direct from BLAST+ may differ in the presence of XXXX masking on regions |
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192 low complexity (columns 21 and 22), and thus also calculated figures like |
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193 the percentage identity (column 3). |
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194 |
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195 **References** |
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196 |
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197 If you use this Galaxy tool in work leading to a scientific publication please |
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198 cite: |
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199 |
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200 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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201 Galaxy tools and workflows for sequence analysis with applications |
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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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202 in molecular plant pathology. PeerJ 1:e167 |
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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203 http://dx.doi.org/10.7717/peerj.167 |
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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204 |
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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205 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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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206 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
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643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
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207 </help> |
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2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
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208 <citations> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
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209 <citation type="doi">10.7717/peerj.167</citation> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
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210 </citations> |
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643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
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211 </tool> |