Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastx_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 | 6f8ea4b9a2c4 |
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rev | line source |
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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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1 <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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2 <description>Search protein database with translated nucleotide query sequence(s)</description> |
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3 <macros> |
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4 <token name="@BINARY@">blastx</token> |
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5 <import>ncbi_macros.xml</import> |
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6 </macros> |
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v0.1.05 - Update citation information now GigaScience paper is out
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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 blastx |
25 | 13 @QUERY@ |
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14 @BLAST_DB_SUBJECT@ |
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15 -query_gencode $query_gencode |
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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 |
23 | 22 @ADV_MATRIX_GAPCOSTS@ |
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23 @ADV_FILTER_QUERY@ |
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24 @ADV_MAX_HITS@ |
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25 @ADV_WORD_SIZE@ |
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26 $adv_opts.ungapped |
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27 @ADV_ID_LIST_FILTER@ |
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28 @ADV_QCOV_HSP_PERC@ |
23 | 29 @ADV_WINDOW_SIZE@ |
30 @ADV_THRESHOLD@ | |
31 @ADV_COMP_BASED_STATS@ | |
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32 ## End of advanced options: |
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33 #end if |
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34 </command> |
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35 <inputs> |
25 | 36 <expand macro="nucl_query" /> |
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37 |
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38 <expand macro="input_conditional_protein_db" /> |
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39 <expand macro="input_query_gencode" /> |
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40 <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST"> |
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41 <option value="blastx">blastx - Traditional BLASTX to compare translated nucleotide query to protein database</option> |
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42 <option value="blastx-fast">blastx-fast - Use longer words for seeding, faster but less accurate</option> |
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43 </param> |
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44 <expand macro="input_evalue" /> |
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45 |
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46 <expand macro="input_out_format" /> |
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47 <expand macro="advanced_options"> |
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48 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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49 <expand macro="input_filter_query_default_true" /> |
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50 <expand macro="input_strand" /> |
23 | 51 <expand macro="input_matrix_gapcosts" /> |
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52 <expand macro="input_max_hits" /> |
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53 <expand macro="input_word_size" /> |
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54 <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
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55 <expand macro="input_parse_deflines" /> |
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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.
peterjc
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56 <expand macro="advanced_optional_id_files" /> |
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57 <expand macro="input_qcov_hsp_perc" /> |
23 | 58 <expand macro="input_window_size" /> |
59 <expand macro="input_threshold" /> | |
60 <expand macro="input_comp_based_stats" /> | |
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61 </expand> |
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62 </inputs> |
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63 <outputs> |
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64 <data name="output1" format="tabular" label="blastx $query.name vs @ON_DB_SUBJECT@"> |
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65 <expand macro="output_change_format" /> |
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66 </data> |
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67 </outputs> |
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68 <tests> |
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69 <test> |
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70 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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71 <param name="db_opts_selector" value="file" /> |
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72 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
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73 <param name="database" value="" /> |
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74 <param name="evalue_cutoff" value="1e-10" /> |
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75 <param name="out_format" value="5" /> |
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76 <param name="adv_opts_selector" value="basic" /> |
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77 <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> |
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78 </test> |
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79 <test> |
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80 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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81 <param name="db_opts_selector" value="file" /> |
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82 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
643338ac83c0
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83 <param name="database" value="" /> |
643338ac83c0
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84 <param name="evalue_cutoff" value="1e-10" /> |
643338ac83c0
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85 <param name="out_format" value="6" /> |
643338ac83c0
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86 <param name="adv_opts_selector" value="basic" /> |
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87 <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" /> |
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88 </test> |
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89 <test> |
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90 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
643338ac83c0
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91 <param name="db_opts_selector" value="file" /> |
643338ac83c0
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92 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
643338ac83c0
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peterjc
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93 <param name="database" value="" /> |
643338ac83c0
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94 <param name="evalue_cutoff" value="1e-10" /> |
643338ac83c0
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95 <param name="out_format" value="ext" /> |
643338ac83c0
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96 <param name="adv_opts_selector" value="basic" /> |
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97 <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" /> |
643338ac83c0
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98 </test> |
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99 <test> |
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100 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
623f727cdff1
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101 <param name="db_opts_selector" value="file" /> |
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102 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
623f727cdff1
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103 <param name="database" value="" /> |
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104 <param name="evalue_cutoff" value="1e-10" /> |
623f727cdff1
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105 <param name="out_format" value="cols" /> |
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106 <param name="std_cols" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" /> |
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107 <param name="ext_cols" value="sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" /> |
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108 <param name="ids_cols" value="qgi,qacc,qaccver,sallseqid,sgi,sallgi,sacc,saccver,sallacc,stitle" /> |
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109 <param name="misc_cols" value="sstrand,frames,btop,qcovs,qcovhsp" /> |
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110 <param name="tax_cols" value="staxids,sscinames,scomnames,sblastnames,sskingdoms" /> |
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111 <param name="adv_opts_selector" value="basic" /> |
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112 <output name="output1" file="blastx_rhodopsin_vs_four_human_all.tabular" ftype="tabular" /> |
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113 </test> |
23 | 114 <test> |
115 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> | |
116 <param name="db_opts_selector" value="file" /> | |
117 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> | |
118 <param name="database" value="" /> | |
119 <param name="evalue_cutoff" value="1e-10" /> | |
120 <param name="out_format" value="6" /> | |
121 <param name="adv_opts_selector" value="advanced" /> | |
122 <param name="matrix" value="BLOSUM62" /> | |
123 <output name="output1" file="blastx_rhodopsin_adv_vs_four_human.tabular" ftype="tabular" /> | |
124 </test> | |
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125 </tests> |
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126 <help> |
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127 |
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128 @SEARCH_TIME_WARNING@ |
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129 |
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130 **What it does** |
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131 |
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132 Search a *protein database* using a *translated nucleotide query*, |
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133 using the NCBI BLAST+ blastx command line tool. |
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134 |
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135 @FASTA_WARNING@ |
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136 |
23 | 137 ------- |
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138 |
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139 @OUTPUT_FORMAT@ |
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140 |
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141 ------- |
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142 |
23 | 143 @CLI_OPTIONS@ |
144 | |
145 ------- | |
146 | |
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147 **References** |
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148 |
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149 If you use this Galaxy tool in work leading to a scientific publication please |
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150 cite the following papers: |
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151 |
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152 @REFERENCES@ |
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153 </help> |
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154 <expand macro="blast_citations" /> |
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155 </tool> |