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1 <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.12">
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2 <description>Search translated nucleotide database with protein 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" shared_inputs="subject" merge_outputs="output1"></parallelism>
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5 <version_command>tblastn -version</version_command>
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6 <command interpreter="python">hide_stderr.py
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7 ## The command is a Cheetah template which allows some Python based syntax.
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8 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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9 tblastn
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10 -query "$query"
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11 #if $db_opts.db_opts_selector == "db":
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12 -db "${db_opts.database.fields.path}"
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13 #else:
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14 -subject "$db_opts.subject"
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15 #end if
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16 -evalue $evalue_cutoff
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17 -out $output1
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18 ##Set the extended list here so if/when we add things, saved workflows are not affected
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19 #if str($out_format)=="ext":
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20 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
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21 #else:
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22 -outfmt $out_format
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23 #end if
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24 -num_threads 8
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25 #if $adv_opts.adv_opts_selector=="advanced":
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26 -db_gencode $adv_opts.db_gencode
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27 $adv_opts.filter_query
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28 -matrix $adv_opts.matrix
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29 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
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30 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
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31 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
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32 -max_target_seqs $adv_opts.max_hits
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33 #end if
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34 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
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35 -word_size $adv_opts.word_size
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36 #end if
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37 ##Ungapped disabled for now - see comments below
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38 ##$adv_opts.ungapped
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39 $adv_opts.parse_deflines
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40 ## End of advanced options:
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41 #end if
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42 </command>
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43 <inputs>
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44 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>
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45 <conditional name="db_opts">
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46 <param name="db_opts_selector" type="select" label="Subject database/sequences">
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47 <option value="db" selected="True">BLAST Database</option>
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48 <option value="file">FASTA file (pairwise e-values)</option>
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49 </param>
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50 <when value="db">
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51 <param name="database" type="select" label="Nucleotide BLAST database">
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52 <options from_file="blastdb.loc">
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53 <column name="value" index="0"/>
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54 <column name="name" index="1"/>
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55 <column name="path" index="2"/>
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56 </options>
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57 </param>
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58 <param name="subject" type="hidden" value="" />
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59 </when>
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60 <when value="file">
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61 <param name="database" type="hidden" value="" />
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62 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
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63 </when>
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64 </conditional>
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65 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
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66 <param name="out_format" type="select" label="Output format">
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67 <option value="6" selected="True">Tabular (standard 12 columns)</option>
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68 <option value="ext">Tabular (extended 24 columns)</option>
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69 <option value="5">BLAST XML</option>
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70 <option value="0">Pairwise text</option>
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71 <option value="0 -html">Pairwise HTML</option>
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72 <option value="2">Query-anchored text</option>
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73 <option value="2 -html">Query-anchored HTML</option>
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74 <option value="4">Flat query-anchored text</option>
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75 <option value="4 -html">Flat query-anchored HTML</option>
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76 <!--
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77 <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
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78 -->
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79 </param>
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80 <conditional name="adv_opts">
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81 <param name="adv_opts_selector" type="select" label="Advanced Options">
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82 <option value="basic" selected="True">Hide Advanced Options</option>
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83 <option value="advanced">Show Advanced Options</option>
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84 </param>
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85 <when value="basic" />
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86 <when value="advanced">
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87 <param name="db_gencode" type="select" label="Database/subject genetic code">
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88 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
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89 <option value="1" select="True">1. Standard</option>
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90 <option value="2">2. Vertebrate Mitochondrial</option>
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91 <option value="3">3. Yeast Mitochondrial</option>
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92 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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93 <option value="5">5. Invertebrate Mitochondrial</option>
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94 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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95 <option value="9">9. Echinoderm Mitochondrial</option>
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96 <option value="10">10. Euplotid Nuclear</option>
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97 <option value="11">11. Bacteria and Archaea</option>
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98 <option value="12">12. Alternative Yeast Nuclear</option>
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99 <option value="13">13. Ascidian Mitochondrial</option>
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100 <option value="14">14. Flatworm Mitochondrial</option>
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101 <option value="15">15. Blepharisma Macronuclear</option>
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102 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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103 <option value="21">21. Trematode Mitochondrial Code</option>
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104 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
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105 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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106 <option value="24">24. Pterobranchia mitochondrial code</option>
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107 </param>
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108 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
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109 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
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110 <param name="matrix" type="select" label="Scoring matrix">
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111 <option value="BLOSUM90">BLOSUM90</option>
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112 <option value="BLOSUM80">BLOSUM80</option>
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113 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
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114 <option value="BLOSUM50">BLOSUM50</option>
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115 <option value="BLOSUM45">BLOSUM45</option>
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116 <option value="PAM250">PAM250</option>
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117 <option value="PAM70">PAM70</option>
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118 <option value="PAM30">PAM30</option>
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119 </param>
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120 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
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121 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
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122 <validator type="in_range" min="0" />
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123 </param>
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124 <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
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125 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
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126 <validator type="in_range" min="0" />
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127 </param>
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128 <!--
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129 Can't use '-ungapped' on its own, error back is:
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130 Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
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131 Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.'
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132 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
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133 -->
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134 <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
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135 </when>
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136 </conditional>
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137 </inputs>
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138 <outputs>
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139 <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}">
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140 <change_format>
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141 <when input="out_format" value="0" format="txt"/>
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142 <when input="out_format" value="0 -html" format="html"/>
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143 <when input="out_format" value="2" format="txt"/>
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144 <when input="out_format" value="2 -html" format="html"/>
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145 <when input="out_format" value="4" format="txt"/>
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146 <when input="out_format" value="4 -html" format="html"/>
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147 <when input="out_format" value="5" format="blastxml"/>
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148 </change_format>
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149 </data>
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150 </outputs>
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151 <requirements>
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152 <requirement type="binary">tblastn</requirement>
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153 </requirements>
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154 <tests>
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155 <test>
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156 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
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157 <param name="db_opts_selector" value="file" />
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158 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
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159 <param name="database" value="" />
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160 <param name="evalue_cutoff" value="1e-10" />
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161 <param name="out_format" value="5" />
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162 <param name="adv_opts_selector" value="advanced" />
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163 <param name="filter_query" value="false" />
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164 <param name="matrix" value="BLOSUM80" />
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165 <param name="max_hits" value="0" />
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166 <param name="word_size" value="0" />
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167 <param name="parse_deflines" value="false" />
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168 <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" />
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169 </test>
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170 <test>
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171 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
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172 <param name="db_opts_selector" value="file" />
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173 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
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174 <param name="database" value="" />
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175 <param name="evalue_cutoff" value="1e-10" />
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176 <param name="out_format" value="ext" />
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177 <param name="adv_opts_selector" value="advanced" />
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178 <param name="filter_query" value="false" />
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179 <param name="matrix" value="BLOSUM80" />
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180 <param name="max_hits" value="0" />
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181 <param name="word_size" value="0" />
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182 <param name="parse_deflines" value="false" />
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183 <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
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184 </test>
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185 <test>
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186 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
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187 <param name="db_opts_selector" value="file" />
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188 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
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189 <param name="database" value="" />
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190 <param name="evalue_cutoff" value="1e-10" />
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191 <param name="out_format" value="6" />
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192 <param name="adv_opts_selector" value="advanced" />
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193 <param name="filter_query" value="false" />
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194 <param name="matrix" value="BLOSUM80" />
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195 <param name="max_hits" value="0" />
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196 <param name="word_size" value="0" />
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197 <param name="parse_deflines" value="false" />
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198 <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
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199 </test>
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200 <test>
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201 <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference -->
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202 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
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203 <param name="db_opts_selector" value="file" />
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204 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
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205 <param name="database" value="" />
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206 <param name="evalue_cutoff" value="1e-10" />
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207 <param name="out_format" value="6" />
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208 <param name="adv_opts_selector" value="advanced" />
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209 <param name="filter_query" value="false" />
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210 <param name="matrix" value="BLOSUM80" />
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211 <param name="max_hits" value="0" />
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212 <param name="word_size" value="0" />
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213 <param name="parse_deflines" value="true" />
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214 <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
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215 </test>
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216 <test>
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217 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
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218 <param name="db_opts_selector" value="file" />
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219 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
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220 <param name="database" value="" />
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221 <param name="evalue_cutoff" value="1e-10" />
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222 <param name="out_format" value="0 -html" />
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223 <param name="adv_opts_selector" value="advanced" />
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224 <param name="filter_query" value="false" />
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225 <param name="matrix" value="BLOSUM80" />
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226 <param name="max_hits" value="0" />
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227 <param name="word_size" value="0" />
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228 <param name="parse_deflines" value="false" />
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229 <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" />
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230 </test>
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231 </tests>
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232 <help>
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233
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234 .. class:: warningmark
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235
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236 **Note**. Database searches may take a substantial amount of time.
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237 For large input datasets it is advisable to allow overnight processing.
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238
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239 -----
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240
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241 **What it does**
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242
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243 Search a *translated nucleotide database* using a *protein query*,
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244 using the NCBI BLAST+ tblastn command line tool.
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245
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246 -----
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247
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248 **Output format**
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249
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250 Because Galaxy focuses on processing tabular data, the default output of this
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251 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
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252
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253 ====== ========= ============================================
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254 Column NCBI name Description
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255 ------ --------- --------------------------------------------
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256 1 qseqid Query Seq-id (ID of your sequence)
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257 2 sseqid Subject Seq-id (ID of the database hit)
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258 3 pident Percentage of identical matches
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259 4 length Alignment length
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260 5 mismatch Number of mismatches
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261 6 gapopen Number of gap openings
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262 7 qstart Start of alignment in query
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263 8 qend End of alignment in query
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264 9 sstart Start of alignment in subject (database hit)
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265 10 send End of alignment in subject (database hit)
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266 11 evalue Expectation value (E-value)
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267 12 bitscore Bit score
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268 ====== ========= ============================================
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269
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270 The BLAST+ tools can optionally output additional columns of information,
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271 but this takes longer to calculate. Most (but not all) of these columns are
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272 included by selecting the extended tabular output. The extra columns are
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273 included *after* the standard 12 columns. This is so that you can write
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274 workflow filtering steps that accept either the 12 or 24 column tabular
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275 BLAST output.
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276
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277 ====== ============= ===========================================
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278 Column NCBI name Description
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279 ------ ------------- -------------------------------------------
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280 13 sallseqid All subject Seq-id(s), separated by a ';'
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281 14 score Raw score
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282 15 nident Number of identical matches
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283 16 positive Number of positive-scoring matches
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284 17 gaps Total number of gaps
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285 18 ppos Percentage of positive-scoring matches
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286 19 qframe Query frame
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287 20 sframe Subject frame
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288 21 qseq Aligned part of query sequence
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289 22 sseq Aligned part of subject sequence
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290 23 qlen Query sequence length
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291 24 slen Subject sequence length
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292 ====== ============= ===========================================
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293
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294 The third option is BLAST XML output, which is designed to be parsed by
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295 another program, and is understood by some Galaxy tools.
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296
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297 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
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298 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
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299 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
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300 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
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301 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
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302
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303 -------
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304
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305 **References**
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306
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307 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
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308
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309 </help>
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310 </tool>
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