Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastn_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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14
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_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.01"> |
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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
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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24 -perc_identity $adv_opts.identity_cutoff |
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.
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25 #end if |
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26 $adv_opts.ungapped |
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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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27 @ADV_ID_LIST_FILTER@ |
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28 ## End of advanced options: |
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29 #end if |
643338ac83c0
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30 </command> |
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31 |
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32 <expand macro="stdio" /> |
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33 |
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34 <inputs> |
643338ac83c0
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35 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> |
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36 |
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37 <expand macro="input_conditional_nucleotide_db" /> |
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38 |
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39 <param name="blast_type" type="select" display="radio" label="Type of BLAST"> |
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40 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option> |
623f727cdff1
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41 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option> |
623f727cdff1
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42 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option> |
623f727cdff1
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43 <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option> |
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44 <!-- Using BLAST 2.2.24+ this gives an error: |
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45 BLAST engine error: Program type 'vecscreen' not supported |
643338ac83c0
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peterjc
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46 <option value="vecscreen">vecscreen</option> |
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47 In any case, vecscreen has gone in BLAST+ 2.2.28 |
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48 --> |
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49 <!-- BLAST+ 2.2.28 also offers rmblastn --> |
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50 </param> |
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51 <expand macro="input_evalue" /> |
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52 <expand macro="input_out_format" /> |
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53 <expand macro="advanced_options"> |
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54 <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> |
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55 <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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56 <expand macro="input_strand" /> |
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57 <expand macro="input_max_hits" /> |
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58 <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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59 |
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60 <!-- I'd like word_size to be optional, with minimum 4 for blastn --> |
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61 <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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62 <validator type="in_range" min="0" /> |
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63 </param> |
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64 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
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65 <expand macro="input_parse_deflines" /> |
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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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66 <expand macro="advanced_optional_id_files" /> |
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67 </expand> |
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68 </inputs> |
643338ac83c0
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69 <outputs> |
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70 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> |
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71 <expand macro="output_change_format" /> |
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72 </data> |
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73 </outputs> |
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74 <tests> |
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75 <test> |
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76 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
70e7dcbf6573
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77 <param name="db_opts_selector" value="file" /> |
70e7dcbf6573
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78 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
70e7dcbf6573
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79 <param name="database" value="" /> |
70e7dcbf6573
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80 <param name="evalue_cutoff" value="1e-40" /> |
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81 <param name="out_format" value="5" /> |
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82 <param name="adv_opts_selector" value="basic" /> |
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83 <output name="output1" file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> |
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84 </test> |
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85 <test> |
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86 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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87 <param name="db_opts_selector" value="file" /> |
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88 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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89 <param name="database" value="" /> |
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90 <param name="evalue_cutoff" value="1e-40" /> |
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91 <param name="out_format" value="6" /> |
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.
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92 <param name="adv_opts_selector" value="basic" /> |
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93 <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" /> |
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94 </test> |
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95 <test> |
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96 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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97 <param name="db_opts_selector" value="file" /> |
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98 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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99 <param name="database" value="" /> |
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100 <param name="evalue_cutoff" value="1e-40" /> |
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101 <param name="out_format" value="cols" /> |
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102 <param name="std_cols" value="qseqid,sseqid,pident" /> |
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103 <param name="ext_cols" value="qlen,slen" /> |
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104 <param name="adv_opts_selector" value="basic" /> |
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105 <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> |
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106 </test> |
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107 </tests> |
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108 <help> |
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109 |
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110 @SEARCH_TIME_WARNING@ |
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111 |
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112 **What it does** |
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113 |
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114 Search a *nucleotide database* using a *nucleotide query*, |
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115 using the NCBI BLAST+ blastn command line tool. |
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116 Algorithms include blastn, megablast, and discontiguous megablast. |
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117 |
11
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118 @FASTA_WARNING@ |
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119 |
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120 ----- |
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121 |
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122 @OUTPUT_FORMAT@ |
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123 |
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124 ------- |
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125 |
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126 **References** |
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127 |
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128 If you use this Galaxy tool in work leading to a scientific publication please |
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129 cite the following papers: |
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130 |
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131 @REFERENCES@ |
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132 </help> |
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133 <expand macro="blast_citations" /> |
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134 </tool> |