Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @ 10:70e7dcbf6573 draft
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.
author | peterjc |
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date | Mon, 23 Sep 2013 06:14:13 -0400 |
parents | 9dabbfd73c8a |
children | 4c4a0da938ff |
rev | line source |
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10
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.
peterjc
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1 <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.20"> |
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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,histdb" merge_outputs="output1"></parallelism> |
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5 <requirements> |
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6 <requirement type="binary">tblastn</requirement> |
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7 <requirement type="package" version="2.2.26+">blast+</requirement> |
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8 </requirements> |
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9 <version_command>tblastn -version</version_command> |
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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 tblastn |
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14 -query "$query" |
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15 #if $db_opts.db_opts_selector == "db": |
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16 -db "${db_opts.database.fields.path}" |
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17 #elif $db_opts.db_opts_selector == "histdb": |
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18 -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" |
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19 #else: |
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20 -subject "$db_opts.subject" |
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21 #end if |
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22 -evalue $evalue_cutoff |
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23 -out "$output1" |
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24 ##Set the extended list here so if/when we add things, saved workflows are not affected |
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25 #if str($out_format)=="ext": |
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26 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" |
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27 #else: |
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28 -outfmt $out_format |
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29 #end if |
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30 -num_threads 8 |
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31 #if $adv_opts.adv_opts_selector=="advanced": |
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32 -db_gencode $adv_opts.db_gencode |
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33 $adv_opts.filter_query |
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34 -matrix $adv_opts.matrix |
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35 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
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36 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments |
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37 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
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38 -max_target_seqs $adv_opts.max_hits |
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39 #end if |
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40 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): |
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41 -word_size $adv_opts.word_size |
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42 #end if |
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43 ##Ungapped disabled for now - see comments below |
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44 ##$adv_opts.ungapped |
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45 $adv_opts.parse_deflines |
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46 ## End of advanced options: |
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47 #end if |
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48 </command> |
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49 <stdio> |
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50 <!-- Anything other than zero is an error --> |
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51 <exit_code range="1:" /> |
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52 <exit_code range=":-1" /> |
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53 <!-- In case the return code has not been set propery check stderr too --> |
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54 <regex match="Error:" /> |
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55 <regex match="Exception:" /> |
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56 </stdio> |
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57 <inputs> |
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58 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> |
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59 <conditional name="db_opts"> |
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60 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
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61 <option value="db" selected="True">Locally installed BLAST database</option> |
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62 <option value="histdb">BLAST database from your history</option> |
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63 <option value="file">FASTA file from your history (see warning note below)</option> |
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64 </param> |
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65 <when value="db"> |
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66 <param name="database" type="select" label="Nucleotide BLAST database"> |
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67 <options from_file="blastdb.loc"> |
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68 <column name="value" index="0"/> |
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69 <column name="name" index="1"/> |
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70 <column name="path" index="2"/> |
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71 </options> |
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72 </param> |
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73 <param name="histdb" type="hidden" value="" /> |
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74 <param name="subject" type="hidden" value="" /> |
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75 </when> |
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76 <when value="histdb"> |
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77 <param name="database" type="hidden" value="" /> |
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78 <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> |
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79 <param name="subject" type="hidden" value="" /> |
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80 </when> |
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81 <when value="file"> |
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82 <param name="database" type="hidden" value="" /> |
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83 <param name="histdb" type="hidden" value="" /> |
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84 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> |
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85 </when> |
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86 </conditional> |
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87 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> |
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88 <param name="out_format" type="select" label="Output format"> |
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89 <option value="6">Tabular (standard 12 columns)</option> |
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90 <option value="ext" selected="True">Tabular (extended 24 columns)</option> |
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91 <option value="5">BLAST XML</option> |
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92 <option value="0">Pairwise text</option> |
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93 <option value="0 -html">Pairwise HTML</option> |
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94 <option value="2">Query-anchored text</option> |
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95 <option value="2 -html">Query-anchored HTML</option> |
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96 <option value="4">Flat query-anchored text</option> |
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97 <option value="4 -html">Flat query-anchored HTML</option> |
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98 <!-- |
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99 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
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100 --> |
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101 </param> |
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102 <conditional name="adv_opts"> |
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103 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
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104 <option value="basic" selected="True">Hide Advanced Options</option> |
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105 <option value="advanced">Show Advanced Options</option> |
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106 </param> |
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107 <when value="basic" /> |
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108 <when value="advanced"> |
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109 <param name="db_gencode" type="select" label="Database/subject genetic code"> |
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110 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> |
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111 <option value="1" select="True">1. Standard</option> |
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112 <option value="2">2. Vertebrate Mitochondrial</option> |
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113 <option value="3">3. Yeast Mitochondrial</option> |
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114 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
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115 <option value="5">5. Invertebrate Mitochondrial</option> |
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116 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> |
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117 <option value="9">9. Echinoderm Mitochondrial</option> |
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118 <option value="10">10. Euplotid Nuclear</option> |
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119 <option value="11">11. Bacteria and Archaea</option> |
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120 <option value="12">12. Alternative Yeast Nuclear</option> |
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121 <option value="13">13. Ascidian Mitochondrial</option> |
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122 <option value="14">14. Flatworm Mitochondrial</option> |
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123 <option value="15">15. Blepharisma Macronuclear</option> |
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124 <option value="16">16. Chlorophycean Mitochondrial Code</option> |
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125 <option value="21">21. Trematode Mitochondrial Code</option> |
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126 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> |
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127 <option value="23">23. Thraustochytrium Mitochondrial Code</option> |
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128 <option value="24">24. Pterobranchia mitochondrial code</option> |
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129 </param> |
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130 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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131 <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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132 <param name="matrix" type="select" label="Scoring matrix"> |
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133 <option value="BLOSUM90">BLOSUM90</option> |
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134 <option value="BLOSUM80">BLOSUM80</option> |
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135 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> |
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136 <option value="BLOSUM50">BLOSUM50</option> |
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137 <option value="BLOSUM45">BLOSUM45</option> |
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138 <option value="PAM250">PAM250</option> |
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139 <option value="PAM70">PAM70</option> |
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140 <option value="PAM30">PAM30</option> |
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141 </param> |
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142 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> |
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143 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> |
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144 <validator type="in_range" min="0" /> |
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145 </param> |
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146 <!-- I'd like word_size to be optional, with minimum 2 for blastp --> |
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147 <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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148 <validator type="in_range" min="0" /> |
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149 </param> |
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150 <!-- |
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151 Can't use '-ungapped' on its own, error back is: |
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152 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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153 Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.' |
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154 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> |
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155 --> |
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156 <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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157 </when> |
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158 </conditional> |
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159 </inputs> |
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160 <outputs> |
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161 <data name="output1" format="tabular" label="tblastn on ${on_string}"> |
3
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162 <change_format> |
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163 <when input="out_format" value="0" format="txt"/> |
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164 <when input="out_format" value="0 -html" format="html"/> |
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165 <when input="out_format" value="2" format="txt"/> |
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166 <when input="out_format" value="2 -html" format="html"/> |
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167 <when input="out_format" value="4" format="txt"/> |
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168 <when input="out_format" value="4 -html" format="html"/> |
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169 <when input="out_format" value="5" format="blastxml"/> |
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170 </change_format> |
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171 </data> |
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172 </outputs> |
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173 <tests> |
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174 <test> |
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175 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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176 <param name="db_opts_selector" value="file" /> |
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177 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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178 <param name="database" value="" /> |
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179 <param name="evalue_cutoff" value="1e-10" /> |
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180 <param name="out_format" value="5" /> |
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181 <param name="adv_opts_selector" value="advanced" /> |
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182 <param name="filter_query" value="false" /> |
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183 <param name="matrix" value="BLOSUM80" /> |
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184 <param name="max_hits" value="0" /> |
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185 <param name="word_size" value="0" /> |
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186 <param name="parse_deflines" value="false" /> |
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187 <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" /> |
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188 </test> |
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189 <test> |
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190 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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191 <param name="db_opts_selector" value="file" /> |
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192 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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193 <param name="database" value="" /> |
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194 <param name="evalue_cutoff" value="1e-10" /> |
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195 <param name="out_format" value="ext" /> |
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196 <param name="adv_opts_selector" value="advanced" /> |
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197 <param name="filter_query" value="false" /> |
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198 <param name="matrix" value="BLOSUM80" /> |
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199 <param name="max_hits" value="0" /> |
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200 <param name="word_size" value="0" /> |
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201 <param name="parse_deflines" value="false" /> |
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202 <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> |
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203 </test> |
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204 <test> |
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205 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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206 <param name="db_opts_selector" value="file" /> |
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207 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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208 <param name="database" value="" /> |
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209 <param name="evalue_cutoff" value="1e-10" /> |
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210 <param name="out_format" value="6" /> |
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211 <param name="adv_opts_selector" value="advanced" /> |
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212 <param name="filter_query" value="false" /> |
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213 <param name="matrix" value="BLOSUM80" /> |
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214 <param name="max_hits" value="0" /> |
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215 <param name="word_size" value="0" /> |
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216 <param name="parse_deflines" value="false" /> |
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217 <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> |
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218 </test> |
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219 <test> |
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220 <!-- Same as above, but parse deflines - on BLAST 2.2.25+ - 2.2.27+ makes no difference --> |
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221 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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222 <param name="db_opts_selector" value="file" /> |
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223 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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224 <param name="database" value="" /> |
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225 <param name="evalue_cutoff" value="1e-10" /> |
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226 <param name="out_format" value="6" /> |
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227 <param name="adv_opts_selector" value="advanced" /> |
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228 <param name="filter_query" value="false" /> |
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229 <param name="matrix" value="BLOSUM80" /> |
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230 <param name="max_hits" value="0" /> |
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231 <param name="word_size" value="0" /> |
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232 <param name="parse_deflines" value="true" /> |
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233 <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> |
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234 </test> |
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235 <test> |
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236 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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237 <param name="db_opts_selector" value="file" /> |
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238 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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239 <param name="database" value="" /> |
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240 <param name="evalue_cutoff" value="1e-10" /> |
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241 <param name="out_format" value="0 -html" /> |
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242 <param name="adv_opts_selector" value="advanced" /> |
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243 <param name="filter_query" value="false" /> |
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244 <param name="matrix" value="BLOSUM80" /> |
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245 <param name="max_hits" value="0" /> |
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246 <param name="word_size" value="0" /> |
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247 <param name="parse_deflines" value="false" /> |
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248 <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" /> |
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249 </test> |
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250 </tests> |
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251 <help> |
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252 |
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253 .. class:: warningmark |
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254 |
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255 **Note**. Database searches may take a substantial amount of time. |
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256 For large input datasets it is advisable to allow overnight processing. |
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257 |
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258 ----- |
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259 |
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260 **What it does** |
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261 |
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262 Search a *translated nucleotide database* using a *protein query*, |
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263 using the NCBI BLAST+ tblastn command line tool. |
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264 |
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265 .. class:: warningmark |
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266 |
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267 You can also search against a FASTA file of subject nucleotide |
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268 sequences. This is *not* advised because it is slower (only one |
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269 CPU is used), but more importantly gives e-values for pairwise |
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270 searches (very small e-values which will look overly signficiant). |
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271 In most cases you should instead turn the other FASTA file into a |
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272 database first using *makeblastdb* and search against that. |
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273 |
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274 ----- |
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275 |
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276 **Output format** |
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277 |
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278 Because Galaxy focuses on processing tabular data, the default output of this |
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279 tool is tabular. The standard BLAST+ tabular output contains 12 columns: |
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280 |
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281 ====== ========= ============================================ |
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282 Column NCBI name Description |
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283 ------ --------- -------------------------------------------- |
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284 1 qseqid Query Seq-id (ID of your sequence) |
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285 2 sseqid Subject Seq-id (ID of the database hit) |
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286 3 pident Percentage of identical matches |
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287 4 length Alignment length |
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288 5 mismatch Number of mismatches |
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289 6 gapopen Number of gap openings |
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290 7 qstart Start of alignment in query |
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291 8 qend End of alignment in query |
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292 9 sstart Start of alignment in subject (database hit) |
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293 10 send End of alignment in subject (database hit) |
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294 11 evalue Expectation value (E-value) |
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295 12 bitscore Bit score |
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296 ====== ========= ============================================ |
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297 |
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298 The BLAST+ tools can optionally output additional columns of information, |
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299 but this takes longer to calculate. Most (but not all) of these columns are |
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300 included by selecting the extended tabular output. The extra columns are |
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301 included *after* the standard 12 columns. This is so that you can write |
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302 workflow filtering steps that accept either the 12 or 24 column tabular |
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303 BLAST output. Galaxy now uses this extended 24 column output by default. |
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304 |
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305 ====== ============= =========================================== |
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306 Column NCBI name Description |
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307 ------ ------------- ------------------------------------------- |
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308 13 sallseqid All subject Seq-id(s), separated by a ';' |
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309 14 score Raw score |
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310 15 nident Number of identical matches |
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311 16 positive Number of positive-scoring matches |
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312 17 gaps Total number of gaps |
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313 18 ppos Percentage of positive-scoring matches |
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314 19 qframe Query frame |
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315 20 sframe Subject frame |
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316 21 qseq Aligned part of query sequence |
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317 22 sseq Aligned part of subject sequence |
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318 23 qlen Query sequence length |
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319 24 slen Subject sequence length |
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320 ====== ============= =========================================== |
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321 |
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322 The third option is BLAST XML output, which is designed to be parsed by |
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323 another program, and is understood by some Galaxy tools. |
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324 |
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325 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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326 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
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327 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
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328 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
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329 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
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330 |
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331 ------- |
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332 |
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333 **References** |
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334 |
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335 If you use this Galaxy tool in work leading to a scientific publication please |
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336 cite the following papers: |
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337 |
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338 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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339 Galaxy tools and workflows for sequence analysis with applications |
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340 in molecular plant pathology. PeerJ 1:e167 |
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341 http://dx.doi.org/10.7717/peerj.167 |
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342 |
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343 Christiam Camacho et al. (2009). |
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344 BLAST+: architecture and applications. |
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345 BMC Bioinformatics. 15;10:421. |
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346 http://dx.doi.org/10.1186/1471-2105-10-421 |
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347 |
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348 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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349 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
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350 </help> |
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351 </tool> |