Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 11:4c4a0da938ff draft
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
Supports $GALAXY_SLOTS.
Includes more tests and heavy use of macros.
author | peterjc |
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date | Thu, 05 Dec 2013 06:55:59 -0500 |
parents | 70e7dcbf6573 |
children | 623f727cdff1 |
rev | line source |
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11
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1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.22"> |
3
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2 <description>Search nucleotide database with nucleotide query sequence(s)</description> |
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3 <!-- If job splitting is enabled, break up the query file into parts --> |
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4 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> |
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5 <macros> |
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6 <token name="@BINARY@">blastn</token> |
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7 <import>ncbi_macros.xml</import> |
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8 </macros> |
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9 <expand macro="requirements" /> |
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10 <command> |
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11 ## The command is a Cheetah template which allows some Python based syntax. |
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12 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
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13 blastn |
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14 -query "$query" |
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15 @BLAST_DB_SUBJECT@ |
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16 -task $blast_type |
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17 -evalue $evalue_cutoff |
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18 @BLAST_OUTPUT@ |
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19 @THREADS@ |
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20 #if $adv_opts.adv_opts_selector=="advanced": |
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21 $adv_opts.strand |
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22 @ADVANCED_OPTIONS@ |
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23 #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): |
70e7dcbf6573
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24 -perc_identity $adv_opts.identity_cutoff |
70e7dcbf6573
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25 #end if |
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26 $adv_opts.ungapped |
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27 ## End of advanced options: |
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28 #end if |
643338ac83c0
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29 </command> |
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30 |
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31 <expand macro="stdio" /> |
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32 |
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33 <inputs> |
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34 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> |
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35 |
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36 <expand macro="input_conditional_nucleotide_db" /> |
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37 |
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38 <param name="blast_type" type="select" display="radio" label="Type of BLAST"> |
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39 <option value="megablast">megablast</option> |
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40 <option value="blastn">blastn</option> |
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41 <option value="blastn-short">blastn-short</option> |
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42 <option value="dc-megablast">dc-megablast</option> |
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43 <!-- Using BLAST 2.2.24+ this gives an error: |
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44 BLAST engine error: Program type 'vecscreen' not supported |
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45 <option value="vecscreen">vecscreen</option> |
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46 --> |
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47 </param> |
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48 <expand macro="input_evalue" /> |
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49 <expand macro="input_out_format" /> |
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50 <expand macro="advanced_options"> |
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51 <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> |
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52 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> |
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53 <expand macro="input_strand" /> |
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54 <expand macro="input_max_hits" /> |
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55 <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" /> |
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56 |
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57 <!-- I'd like word_size to be optional, with minimum 4 for blastn --> |
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58 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> |
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59 <validator type="in_range" min="0" /> |
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60 </param> |
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61 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
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62 <expand macro="input_parse_deflines" /> |
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63 </expand> |
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64 </inputs> |
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65 <outputs> |
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66 <data name="output1" format="tabular" label="${blast_type.value_label} $query.name vs @ON_DB_SUBJECT@"> |
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67 <expand macro="output_change_format" /> |
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68 </data> |
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69 </outputs> |
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70 <tests> |
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71 <test> |
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72 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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73 <param name="db_opts_selector" value="file" /> |
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74 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
70e7dcbf6573
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75 <param name="database" value="" /> |
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76 <param name="evalue_cutoff" value="1e-40" /> |
70e7dcbf6573
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77 <param name="out_format" value="6" /> |
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78 <param name="adv_opts_selector" value="basic" /> |
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79 <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" /> |
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80 </test> |
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81 </tests> |
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82 <help> |
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83 |
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84 @SEARCH_TIME_WARNING@ |
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85 |
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86 **What it does** |
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87 |
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88 Search a *nucleotide database* using a *nucleotide query*, |
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89 using the NCBI BLAST+ blastn command line tool. |
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90 Algorithms include blastn, megablast, and discontiguous megablast. |
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91 |
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92 @FASTA_WARNING@ |
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93 |
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94 ----- |
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95 |
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96 @OUTPUT_FORMAT@ |
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97 |
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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 ------- |
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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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99 |
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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100 **References** |
643338ac83c0
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peterjc
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101 |
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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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102 If you use this Galaxy tool in work leading to a scientific publication please |
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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103 cite the following papers: |
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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104 |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
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105 @REFERENCES@ |
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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
parents:
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106 </help> |
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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107 </tool> |