Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/blastxml_to_tabular.xml @ 13:623f727cdff1 draft
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
author | peterjc |
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date | Fri, 14 Mar 2014 07:40:46 -0400 |
parents | 4c4a0da938ff |
children | 2fe07f50a41e |
rev | line source |
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13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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1 <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.1.00"> |
3
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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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
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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4 <command interpreter="python"> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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5 blastxml_to_tabular.py -o "$tabular_file" |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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6 #if $output.out_format == "cols": |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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7 #set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", " ").replace(",,", ",").replace(",", " ") |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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8 -c "$cols" |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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9 #else |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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10 -c "$output.out_format" |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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11 #end if |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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12 #for i in $blastxml_file#${i} #end for# |
3
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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13 </command> |
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1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
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14 <stdio> |
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
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15 <!-- Anything other than zero is an error --> |
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
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16 <exit_code range="1:" /> |
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
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17 <exit_code range=":-1" /> |
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
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18 </stdio> |
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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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19 <inputs> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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20 <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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21 <conditional name="output"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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22 <param name="out_format" type="select" label="Output format"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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23 <option value="std" selected="True">Tabular (standard 12 columns)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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24 <option value="ext">Tabular (extended 25 columns)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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25 <option value="cols">Tabular (select columns to output)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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26 </param> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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27 <when value="std"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
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28 <when value="ext"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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29 <when value="cols"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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30 <param name="std_cols" type="select" multiple="true" display="checkboxes" label="Standard columns"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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31 <option selected="true" value="qseqid">qseqid = Query Seq-id (ID of your sequence)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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32 <option selected="true" value="sseqid">sseqid = Subject Seq-id (ID of the database hit)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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33 <option selected="true" value="pident">pident = Percentage of identical matches</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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34 <option selected="true" value="length">length = Alignment length</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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35 <option selected="true" value="mismatch">mismatch = Number of mismatches</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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36 <option selected="true" value="gapopen">gapopen = Number of gap openings</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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37 <option selected="true" value="qstart">qstart = Start of alignment in query</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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38 <option selected="true" value="qend">qend = End of alignment in query</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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39 <option selected="true" value="sstart">sstart = Start of alignment in subject (database hit)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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40 <option selected="true" value="send">send = End of alignment in subject (database hit)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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41 <option selected="true" value="evalue">evalue = Expectation value (E-value)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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42 <option selected="true" value="bitscore">bitscore = Bit score</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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43 </param> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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44 <param name="ext_cols" type="select" multiple="true" display="checkboxes" label="Extended columns"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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45 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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46 <option value="score">score = Raw score</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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47 <option value="nident">nident = Number of identical matches</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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48 <option value="positive">positive = Number of positive-scoring matches</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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49 <option value="gaps">gaps = Total number of gaps</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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50 <option value="ppos">ppos = Percentage of positive-scoring matches</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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51 <option value="qframe">qframe = Query frame</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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52 <option value="sframe">sframe = Subject frame</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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53 <option value="qseq">qseq = Aligned part of query sequence</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
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54 <option value="sseq">sseq = Aligned part of subject sequence</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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55 <option value="qlen">qlen = Query sequence length</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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56 <option value="slen">slen = Subject sequence length</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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57 <option value="salltitles">salltitles = All subject title(s), separated by a '<>'</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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58 </param> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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59 </when> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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60 </conditional> |
3
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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61 </inputs> |
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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62 <outputs> |
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peterjc
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63 <data name="tabular_file" format="tabular" label="$on_string (as tabular)" /> |
3
643338ac83c0
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peterjc
parents:
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64 </outputs> |
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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65 <requirements> |
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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66 </requirements> |
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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67 <tests> |
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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68 <test> |
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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69 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.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:
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70 <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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71 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar --> |
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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72 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" /> |
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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73 </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:
diff
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74 <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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75 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.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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76 <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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77 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar --> |
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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78 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" /> |
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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79 </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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80 <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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81 <param name="blastxml_file" value="blastp_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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82 <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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83 <!-- Note this has some white space differences from the actual blastp 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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84 <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" /> |
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 </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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86 <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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87 <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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88 <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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89 <!-- 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
parents:
diff
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90 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" /> |
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 </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:
diff
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92 <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:
diff
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93 <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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94 <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
changeset
|
95 <!-- 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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96 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" /> |
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97 </test> |
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98 <test> |
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99 <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" /> |
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100 <param name="out_format" value="std" /> |
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101 <!-- Note this has some white space differences from the actual blastx output --> |
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102 <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" /> |
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103 </test> |
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104 <test> |
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105 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> |
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106 <param name="out_format" value="std" /> |
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107 <!-- Note this has some white space differences from the actual blastp output --> |
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108 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" /> |
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109 </test> |
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110 <test> |
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111 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> |
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112 <param name="out_format" value="ext" /> |
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113 <!-- Note this has some white space differences from the actual blastp output --> |
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114 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" /> |
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115 </test> |
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116 <test> |
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117 <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> |
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118 <param name="out_format" value="std" /> |
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119 <output name="tabular_file" file="blastn_arabidopsis.standard.tabular" ftype="tabular" /> |
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120 </test> |
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121 <test> |
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122 <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> |
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123 <param name="out_format" value="ext" /> |
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124 <output name="tabular_file" file="blastn_arabidopsis.extended.tabular" ftype="tabular" /> |
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125 </test> |
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126 <!-- there are some harmless white space differences in our conversion to the BLAST+ output here: --> |
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127 <test> |
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128 <param name="blastxml_file" value="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> |
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129 <param name="out_format" value="std" /> |
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130 <output name="tabular_file" file="blastn_rhodopsin_vs_three_human_converted.tabular" ftype="tabular" /> |
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131 </test> |
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132 <test> |
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133 <param name="blastxml_file" value="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> |
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134 <param name="out_format" value="cols" /> |
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135 <param name="std_cols" value="qseqid,sseqid,pident" /> |
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136 <param name="ext_cols" value="qlen,slen" /> |
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137 <output name="tabular_file" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> |
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138 </test> |
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139 </tests> |
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140 <help> |
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141 |
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142 **What it does** |
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143 |
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144 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of |
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145 formats including tabular and a more detailed XML format. A complex workflow |
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146 may need both the XML and the tabular output - but running BLAST twice is |
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147 slow and wasteful. |
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148 |
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149 This tool takes the BLAST XML output and can convert it into the |
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150 standard 12 column tabular equivalent: |
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151 |
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152 ====== ========= ============================================ |
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153 Column NCBI name Description |
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154 ------ --------- -------------------------------------------- |
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155 1 qseqid Query Seq-id (ID of your sequence) |
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156 2 sseqid Subject Seq-id (ID of the database hit) |
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157 3 pident Percentage of identical matches |
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158 4 length Alignment length |
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159 5 mismatch Number of mismatches |
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160 6 gapopen Number of gap openings |
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161 7 qstart Start of alignment in query |
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162 8 qend End of alignment in query |
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163 9 sstart Start of alignment in subject (database hit) |
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164 10 send End of alignment in subject (database hit) |
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165 11 evalue Expectation value (E-value) |
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166 12 bitscore Bit score |
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167 ====== ========= ============================================ |
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168 |
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169 The BLAST+ tools can optionally output additional columns of information, |
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170 but this takes longer to calculate. Most (but not all) of these columns are |
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171 included by selecting the extended tabular output. The extra columns are |
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172 included *after* the standard 12 columns. This is so that you can write |
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173 workflow filtering steps that accept either the 12 or 25 column tabular |
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174 BLAST output. This tool now uses this extended 25 column output by default. |
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175 |
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176 ====== ============= =========================================== |
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177 Column NCBI name Description |
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178 ------ ------------- ------------------------------------------- |
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179 13 sallseqid All subject Seq-id(s), separated by a ';' |
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180 14 score Raw score |
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181 15 nident Number of identical matches |
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182 16 positive Number of positive-scoring matches |
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183 17 gaps Total number of gaps |
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184 18 ppos Percentage of positive-scoring matches |
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185 19 qframe Query frame |
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186 20 sframe Subject frame |
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187 21 qseq Aligned part of query sequence |
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188 22 sseq Aligned part of subject sequence |
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189 23 qlen Query sequence length |
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190 24 slen Subject sequence length |
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191 25 salltitles All subject title(s), separated by a '<>' |
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192 ====== ============= =========================================== |
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193 |
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194 Beware that the XML file (and thus the conversion) and the tabular output |
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195 direct from BLAST+ may differ in the presence of XXXX masking on regions |
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196 low complexity (columns 21 and 22), and thus also calculated figures like |
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197 the percentage identity (column 3). |
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198 |
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199 **References** |
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200 |
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201 If you use this Galaxy tool in work leading to a scientific publication please |
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202 cite: |
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203 |
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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.
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204 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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205 Galaxy tools and workflows for sequence analysis with applications |
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206 in molecular plant pathology. PeerJ 1:e167 |
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207 http://dx.doi.org/10.7717/peerj.167 |
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208 |
70e7dcbf6573
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209 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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210 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
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211 </help> |
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212 </tool> |