Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml @ 14:2fe07f50a41e draft
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.
author | peterjc |
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date | Mon, 01 Dec 2014 05:59:16 -0500 |
parents | 623f727cdff1 |
children | c16c30e9ad5b |
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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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1 <tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.01"> |
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2 <description>Search protein domain database (PSSMs) with protein 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" /> |
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5 <macros> |
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6 <token name="@BINARY@">deltablast</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 rpsblast |
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14 -query "$query" |
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15 #if $db_opts.db_opts_selector == "db": |
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16 -db "${db_opts.database.fields.path}" |
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17 #elif $db_opts.db_opts_selector == "histdb": |
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18 -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" |
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19 #end if |
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20 -evalue $evalue_cutoff |
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21 @BLAST_OUTPUT@ |
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22 @THREADS@ |
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23 #if $adv_opts.adv_opts_selector=="advanced": |
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24 @ADVANCED_OPTIONS@ |
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25 ## End of advanced options: |
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26 #end if |
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27 </command> |
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28 |
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29 <expand macro="stdio" /> |
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30 |
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31 <inputs> |
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32 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> |
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33 |
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34 <expand macro="input_conditional_pssm" /> |
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35 |
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36 <expand macro="input_evalue" /> |
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37 |
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38 <expand macro="input_out_format" /> |
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39 |
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40 <expand macro="advanced_options"> |
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41 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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42 <expand macro="input_filter_query_default_false" /> |
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43 <expand macro="input_max_hits" /> |
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44 <expand macro="input_word_size" /> |
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45 <expand macro="input_parse_deflines" /> |
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46 </expand> |
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47 </inputs> |
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48 <outputs> |
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49 <data name="output1" format="tabular" label="rpsblast on ${on_string}"> |
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50 |
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51 <expand macro="output_change_format" /> |
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52 |
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53 </data> |
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54 </outputs> |
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55 <help> |
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56 |
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57 @SEARCH_TIME_WARNING@ |
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58 |
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59 **What it does** |
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60 |
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61 Search a *protein domain database* using a *protein query*, |
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62 using the NCBI BLAST+ rpsblast command line tool. |
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63 |
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64 The protein domain databases use position-specific scoring matrices |
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65 (PSSMs) and are available for a number of domain collections including: |
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66 |
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67 *CDD* - NCBI curarated meta-collection of domains, see |
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68 http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains |
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69 |
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70 *Kog* - PSSMs from automatically aligned sequences and sequence |
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71 fragments classified in the KOGs resource, the eukaryotic |
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72 counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/new/ |
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73 |
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74 *Cog* - PSSMs from automatically aligned sequences and sequence |
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75 fragments classified in the COGs resource, which focuses primarily |
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76 on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/new/ |
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77 |
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78 *Pfam* - PSSMs from Pfam-A seed alignment database, see |
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79 http://pfam.sanger.ac.uk/ |
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80 |
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81 *Smart* - PSSMs from SMART domain alignment database, see |
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82 http://smart.embl-heidelberg.de/ |
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83 |
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84 *Tigr* - PSSMs from TIGRFAM database of protein families, see |
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85 http://www.jcvi.org/cms/research/projects/tigrfams/overview/ |
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86 |
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87 *Prk* - PSSms from automatically aligned stable clusters in the |
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88 Protein Clusters database, see |
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89 http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters |
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90 |
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91 The exact list of domain databases offered will depend on how your |
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92 local Galaxy has been configured. |
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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 v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
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98 ------- |
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99 |
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100 **References** |
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101 |
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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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102 If you use this Galaxy tool in work leading to a scientific publication please |
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103 cite the following papers: |
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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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104 |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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105 @REFERENCES@ |
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106 </help> |
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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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107 <expand macro="blast_citations" /> |
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108 </tool> |