Mercurial > repos > devteam > ncbi_blast_plus

annotate tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml @ 18:6b0349dce175 draft

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v0.2.00, dropping never-used dependency tags
author peterjc
date Wed, 19 Apr 2017 05:11:30 -0400
parents d8f2c1f560ec
children c5f20ca77de2
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1 <tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="@WRAPPER_VERSION@">
0
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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" />
3
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
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8 <expand macro="preamble" />
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9 <command>
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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 name="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&amp;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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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>