Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml @ 35:cbf3f518b668 draft default tip
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 45f13845a19ba74f7a6284cc06371ec64213d832
author | peterjc |
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date | Thu, 22 Feb 2024 15:07:36 +0000 |
parents | a52d2d93e595 |
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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
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1 <tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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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 |
25 | 13 @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@ |
23 | 26 @ADV_WINDOW_SIZE@ |
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27 ## End of advanced options: |
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28 #end if |
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29 </command> |
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30 <inputs> |
25 | 31 <expand macro="prot_query" /> |
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32 |
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33 <expand macro="input_conditional_pssm" /> |
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34 |
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35 <expand macro="input_evalue" /> |
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36 |
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37 <expand macro="input_out_format" /> |
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38 |
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39 <expand macro="advanced_options"> |
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40 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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41 <expand macro="input_filter_query_default_false" /> |
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42 <expand macro="input_max_hits" /> |
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43 <expand macro="input_parse_deflines" /> |
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44 <expand macro="input_qcov_hsp_perc" /> |
23 | 45 <expand macro="input_window_size" /> |
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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 <tests> |
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56 <test> |
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57 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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58 <param name="db_opts_selector" value="db" /> |
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59 <param name="database" value="cd00003_and_cd00008" /> |
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60 <param name="evalue_cutoff" value="1e-8" /> |
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61 <param name="out_format" value="6" /> |
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62 <output name="output1" file="empty_file.dat" ftype="tabular" /> |
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63 </test> |
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64 </tests> |
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65 <help> |
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66 |
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67 @SEARCH_TIME_WARNING@ |
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68 |
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69 **What it does** |
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70 |
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71 Search a *protein domain database* using a *protein query*, |
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72 using the NCBI BLAST+ rpsblast command line tool. |
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73 |
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74 The protein domain databases use position-specific scoring matrices |
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75 (PSSMs) and are available for a number of domain collections including: |
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76 |
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77 *CDD* - NCBI curarated meta-collection of domains, see |
23 | 78 https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains |
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79 |
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80 *Kog* - PSSMs from automatically aligned sequences and sequence |
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81 fragments classified in the KOGs resource, the eukaryotic |
23 | 82 counterpart to COGs, see https://www.ncbi.nlm.nih.gov/COG/ |
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83 |
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84 *Cog* - PSSMs from automatically aligned sequences and sequence |
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85 fragments classified in the COGs resource, which focuses primarily |
23 | 86 on prokaryotes, see https://www.ncbi.nlm.nih.gov/COG/ |
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87 |
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88 *Pfam* - PSSMs from Pfam-A seed alignment database, see |
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89 http://xfam.org/ |
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90 |
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91 *Smart* - PSSMs from SMART domain alignment database, see |
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92 http://smart.embl-heidelberg.de/ |
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93 |
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94 *Tigr* - PSSMs from TIGRFAM database of protein families, see |
32 | 95 ftp://ftp.jcvi.org/data/TIGRFAMs/ |
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96 |
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97 *Prk* - PSSms from automatically aligned stable clusters in the |
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98 Protein Clusters database, see |
23 | 99 https://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters |
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100 |
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101 The exact list of domain databases offered will depend on how your |
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102 local Galaxy has been configured. |
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103 |
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104 ----- |
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105 |
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106 @OUTPUT_FORMAT@ |
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107 |
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108 ------- |
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109 |
23 | 110 @CLI_OPTIONS@ |
111 | |
112 ------- | |
113 | |
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114 **References** |
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115 |
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116 If you use this Galaxy tool in work leading to a scientific publication please |
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117 cite the following papers: |
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118 |
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119 @REFERENCES@ |
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120 </help> |
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121 <expand macro="blast_citations" /> |
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122 </tool> |