Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.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 | 3034ce97dd33 |
children | 31e517610e1f |
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1 <tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="@WRAPPER_VERSION@"> |
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2 <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> |
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3 <macros> |
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4 <token name="@BINARY@">deltablast</token> |
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5 <import>ncbi_macros.xml</import> |
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6 </macros> |
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7 <expand macro="parallelism" /> |
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8 <expand macro="preamble" /> |
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9 <command detect_errors="aggressive"> |
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10 ## The command is a Cheetah template which allows some Python based syntax. |
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11 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
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12 rpsblast |
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13 -query '$query' |
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14 #if $db_opts.db_opts_selector == "db": |
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15 -db '${db_opts.database.fields.path}' |
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16 #elif $db_opts.db_opts_selector == "histdb": |
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17 -db '${os.path.join($db_opts.histdb.files_path, "blastdb")}' |
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18 #end if |
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19 -evalue $evalue_cutoff |
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20 @BLAST_OUTPUT@ |
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21 @THREADS@ |
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22 #if $adv_opts.adv_opts_selector=="advanced": |
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23 @ADV_FILTER_QUERY@ |
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24 @ADV_MAX_HITS@ |
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25 @ADV_QCOV_HSP_PERC@ |
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26 ## End of advanced options: |
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27 #end if |
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28 </command> |
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29 <inputs> |
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30 <param argument="-query" type="data" format="fasta" label="Protein query sequence(s)"/> |
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31 |
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32 <expand macro="input_conditional_pssm" /> |
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33 |
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34 <expand macro="input_evalue" /> |
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35 |
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36 <expand macro="input_out_format" /> |
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37 |
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38 <expand macro="advanced_options"> |
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39 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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40 <expand macro="input_filter_query_default_false" /> |
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41 <expand macro="input_max_hits" /> |
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42 <expand macro="input_parse_deflines" /> |
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43 <expand macro="input_qcov_hsp_perc" /> |
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44 </expand> |
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45 </inputs> |
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46 <outputs> |
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47 <data name="output1" format="tabular" label="rpsblast on ${on_string}"> |
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48 |
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49 <expand macro="output_change_format" /> |
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50 |
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51 </data> |
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52 </outputs> |
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53 <tests> |
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54 <test> |
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55 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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56 <param name="db_opts_selector" value="db" /> |
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57 <param name="database" value="cd00003_and_cd00008" /> |
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58 <param name="evalue_cutoff" value="1e-8" /> |
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59 <param name="out_format" value="6" /> |
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60 <output name="output1" file="empty_file.dat" ftype="tabular" /> |
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61 </test> |
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62 </tests> |
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63 <help> |
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64 |
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65 @SEARCH_TIME_WARNING@ |
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66 |
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67 **What it does** |
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68 |
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69 Search a *protein domain database* using a *protein query*, |
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70 using the NCBI BLAST+ rpsblast command line tool. |
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71 |
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72 The protein domain databases use position-specific scoring matrices |
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73 (PSSMs) and are available for a number of domain collections including: |
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74 |
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75 *CDD* - NCBI curarated meta-collection of domains, see |
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76 http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains |
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77 |
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78 *Kog* - PSSMs from automatically aligned sequences and sequence |
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79 fragments classified in the KOGs resource, the eukaryotic |
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80 counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/ |
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81 |
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82 *Cog* - PSSMs from automatically aligned sequences and sequence |
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83 fragments classified in the COGs resource, which focuses primarily |
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84 on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/ |
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85 |
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86 *Pfam* - PSSMs from Pfam-A seed alignment database, see |
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87 http://xfam.org/ |
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88 |
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89 *Smart* - PSSMs from SMART domain alignment database, see |
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90 http://smart.embl-heidelberg.de/ |
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91 |
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92 *Tigr* - PSSMs from TIGRFAM database of protein families, see |
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93 http://www.jcvi.org/cms/research/projects/tigrfams/overview/ |
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94 |
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95 *Prk* - PSSms from automatically aligned stable clusters in the |
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96 Protein Clusters database, see |
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97 http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters |
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98 |
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99 The exact list of domain databases offered will depend on how your |
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100 local Galaxy has been configured. |
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101 |
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102 ----- |
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103 |
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104 @OUTPUT_FORMAT@ |
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105 |
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106 ------- |
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107 |
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108 **References** |
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109 |
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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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110 If you use this Galaxy tool in work leading to a scientific publication please |
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111 cite the following papers: |
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112 |
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113 @REFERENCES@ |
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114 </help> |
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115 <expand macro="blast_citations" /> |
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116 </tool> |