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1 <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.12">
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2 <description>Search translated nucleotide database with translated 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" shared_inputs="subject" merge_outputs="output1"></parallelism>
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5 <version_command>tblastx -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 tblastx
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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 -query_gencode $query_gencode
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17 -evalue $evalue_cutoff
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18 -out $output1
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19 ##Set the extended list here so if/when we add things, saved workflows are not affected
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20 #if str($out_format)=="ext":
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21 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
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22 #else:
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23 -outfmt $out_format
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24 #end if
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25 -num_threads 8
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26 #if $adv_opts.adv_opts_selector=="advanced":
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27 -db_gencode $adv_opts.db_gencode
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28 $adv_opts.filter_query
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29 $adv_opts.strand
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30 -matrix $adv_opts.matrix
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31 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
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32 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
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33 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
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34 -max_target_seqs $adv_opts.max_hits
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35 #end if
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36 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
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37 -word_size $adv_opts.word_size
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38 #end if
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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="Nucleotide 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="query_gencode" type="select" label="Query genetic code">
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66 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
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67 <option value="1" select="True">1. Standard</option>
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68 <option value="2">2. Vertebrate Mitochondrial</option>
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69 <option value="3">3. Yeast Mitochondrial</option>
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70 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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71 <option value="5">5. Invertebrate Mitochondrial</option>
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72 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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73 <option value="9">9. Echinoderm Mitochondrial</option>
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74 <option value="10">10. Euplotid Nuclear</option>
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75 <option value="11">11. Bacteria and Archaea</option>
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76 <option value="12">12. Alternative Yeast Nuclear</option>
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77 <option value="13">13. Ascidian Mitochondrial</option>
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78 <option value="14">14. Flatworm Mitochondrial</option>
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79 <option value="15">15. Blepharisma Macronuclear</option>
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80 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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81 <option value="21">21. Trematode Mitochondrial Code</option>
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82 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
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83 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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84 <option value="24">24. Pterobranchia mitochondrial code</option>
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85 </param>
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86 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
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87 <param name="out_format" type="select" label="Output format">
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88 <option value="6" selected="True">Tabular (standard 12 columns)</option>
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89 <option value="ext">Tabular (extended 24 columns)</option>
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90 <option value="5">BLAST XML</option>
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91 <option value="0">Pairwise text</option>
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92 <option value="0 -html">Pairwise HTML</option>
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93 <option value="2">Query-anchored text</option>
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94 <option value="2 -html">Query-anchored HTML</option>
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95 <option value="4">Flat query-anchored text</option>
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96 <option value="4 -html">Flat query-anchored HTML</option>
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97 <!--
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98 <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
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99 -->
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100 </param>
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101 <conditional name="adv_opts">
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102 <param name="adv_opts_selector" type="select" label="Advanced Options">
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103 <option value="basic" selected="True">Hide Advanced Options</option>
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104 <option value="advanced">Show Advanced Options</option>
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105 </param>
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106 <when value="basic" />
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107 <when value="advanced">
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108 <param name="db_gencode" type="select" label="Database/subject genetic code">
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109 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
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110 <option value="1" select="True">1. Standard</option>
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111 <option value="2">2. Vertebrate Mitochondrial</option>
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112 <option value="3">3. Yeast Mitochondrial</option>
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113 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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114 <option value="5">5. Invertebrate Mitochondrial</option>
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115 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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116 <option value="9">9. Echinoderm Mitochondrial</option>
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117 <option value="10">10. Euplotid Nuclear</option>
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118 <option value="11">11. Bacteria and Archaea</option>
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119 <option value="12">12. Alternative Yeast Nuclear</option>
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120 <option value="13">13. Ascidian Mitochondrial</option>
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121 <option value="14">14. Flatworm Mitochondrial</option>
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122 <option value="15">15. Blepharisma Macronuclear</option>
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123 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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124 <option value="21">21. Trematode Mitochondrial Code</option>
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125 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
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126 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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127 <option value="24">24. Pterobranchia mitochondrial code</option>
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128 </param>
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129 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
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130 <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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131 <param name="strand" type="select" label="Query strand(s) to search against database/subject">
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132 <option value="-strand both">Both</option>
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133 <option value="-strand plus">Plus (forward)</option>
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134 <option value="-strand minus">Minus (reverse complement)</option>
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135 </param>
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136 <param name="matrix" type="select" label="Scoring matrix">
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137 <option value="BLOSUM90">BLOSUM90</option>
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138 <option value="BLOSUM80">BLOSUM80</option>
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139 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
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140 <option value="BLOSUM50">BLOSUM50</option>
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141 <option value="BLOSUM45">BLOSUM45</option>
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142 <option value="PAM250">PAM250</option>
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143 <option value="PAM70">PAM70</option>
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144 <option value="PAM30">PAM30</option>
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145 </param>
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146 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
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147 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
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148 <validator type="in_range" min="0" />
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149 </param>
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150 <!-- I'd like word_size to be optional, with minimum 2 for tblastx -->
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151 <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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152 <validator type="in_range" min="0" />
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153 </param>
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154 <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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155 </when>
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156 </conditional>
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157 </inputs>
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158 <outputs>
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159 <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}">
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160 <change_format>
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161 <when input="out_format" value="0" format="txt"/>
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162 <when input="out_format" value="0 -html" format="html"/>
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163 <when input="out_format" value="2" format="txt"/>
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164 <when input="out_format" value="2 -html" format="html"/>
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165 <when input="out_format" value="4" format="txt"/>
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166 <when input="out_format" value="4 -html" format="html"/>
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167 <when input="out_format" value="5" format="blastxml"/>
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168 </change_format>
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169 </data>
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170 </outputs>
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171 <requirements>
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172 <requirement type="binary">tblastx</requirement>
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173 </requirements>
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174 <help>
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175
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176 .. class:: warningmark
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177
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178 **Note**. Database searches may take a substantial amount of time.
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179 For large input datasets it is advisable to allow overnight processing.
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180
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181 -----
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182
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183 **What it does**
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184
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185 Search a *translated nucleotide database* using a *protein query*,
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186 using the NCBI BLAST+ tblastx command line tool.
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187
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188 -----
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189
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190 **Output format**
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191
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192 Because Galaxy focuses on processing tabular data, the default output of this
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193 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
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194
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195 ====== ========= ============================================
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196 Column NCBI name Description
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197 ------ --------- --------------------------------------------
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198 1 qseqid Query Seq-id (ID of your sequence)
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199 2 sseqid Subject Seq-id (ID of the database hit)
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200 3 pident Percentage of identical matches
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201 4 length Alignment length
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202 5 mismatch Number of mismatches
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203 6 gapopen Number of gap openings
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204 7 qstart Start of alignment in query
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205 8 qend End of alignment in query
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206 9 sstart Start of alignment in subject (database hit)
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207 10 send End of alignment in subject (database hit)
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208 11 evalue Expectation value (E-value)
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209 12 bitscore Bit score
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210 ====== ========= ============================================
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211
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212 The BLAST+ tools can optionally output additional columns of information,
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213 but this takes longer to calculate. Most (but not all) of these columns are
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214 included by selecting the extended tabular output. The extra columns are
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215 included *after* the standard 12 columns. This is so that you can write
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216 workflow filtering steps that accept either the 12 or 24 column tabular
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217 BLAST output.
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218
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219 ====== ============= ===========================================
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220 Column NCBI name Description
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221 ------ ------------- -------------------------------------------
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222 13 sallseqid All subject Seq-id(s), separated by a ';'
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223 14 score Raw score
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224 15 nident Number of identical matches
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225 16 positive Number of positive-scoring matches
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226 17 gaps Total number of gaps
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227 18 ppos Percentage of positive-scoring matches
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228 19 qframe Query frame
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229 20 sframe Subject frame
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230 21 qseq Aligned part of query sequence
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231 22 sseq Aligned part of subject sequence
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232 23 qlen Query sequence length
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233 24 slen Subject sequence length
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234 ====== ============= ===========================================
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235
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236 The third option is BLAST XML output, which is designed to be parsed by
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237 another program, and is understood by some Galaxy tools.
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238
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239 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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240 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
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241 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
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242 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
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243 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
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244
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245 -------
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246
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247 **References**
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248
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249 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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250
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251 </help>
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252 </tool>
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