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1 <tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0">
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2 <description>Search protein database with protein query sequence(s)</description>
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3 <!-- If job splitting is enabled, break up the query file into four (This only works if output is tabular) -->
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4 <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
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5 <version_command>blastp -version</version_command>
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6 <requirements>
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7 <requirement type="package" version="333">binaries_for_blast_plus</requirement>
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8 </requirements>
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9 <command>
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10 ## The command is a Cheetah template which allows some Python based syntax.
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11 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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12 blastp
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13 -query "$query"
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14 #if $db_opts.db_opts_selector == "db":
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15 -db "${db_opts.database.fields.path}"
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16 #elif $db_opts.db_opts_selector == "remote":
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17 -db $db_opts.database
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18 -remote
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19 #set $txids = []
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20 #set $ntxids = []
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21 #for $i, $org in enumerate($db_opts.taxid_repeat):
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22 #if $org.exclude:
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23 #set $ntxids = $ntxids + ["txid" + $org.taxid.__str__]
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24 #else
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25 #set $txids = $txids + ["txid" + $org.taxid.__str__]
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26 #end if
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27 #end for
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28 #if (len($txids) + len($ntxids)) > 0:
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29 #set $entrez_query = ''
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30 #if len($txids) > 0:
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31 #set $entrez_query = $entrez_query + '(' + ' OR '.join($txids) + ')'
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32 #end if
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33 #if len($ntxids) > 0:
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34 #set $entrez_query = $entrez_query + ' NOT (' + ' OR '.join($ntxids) + ')'
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35 #end if
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36 -entrez_query '$entrez_query'
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37 #end if
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38 #else:
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39 -subject "$db_opts.subject"
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40 #end if
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41 -task $blast_type
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42 -evalue $evalue_cutoff
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43 -out blast_output
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44 ##Set the extended list here so if/when we add things, saved workflows are not affected
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45 #if str($fmt_opt.out_format)=="text":
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46 -outfmt "$fmt_opt.outfmt" $fmt_opt.html
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47 #if $fmt_opt.num_descriptions.__str__.strip() != '':
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48 -num_descriptions $fmt_opt.num_descriptions
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49 #end if
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50 #if $fmt_opt.num_alignments.__str__.strip() != '':
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51 -num_alignments $fmt_opt.num_alignments
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52 #end if
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53 #else:
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54 -outfmt "$fmt_opt.outfmt"
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55 #if $fmt_opt.max_target_seqs.__str__.strip() != '':
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56 -max_target_seqs $fmt_opt.max_target_seqs
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57 #end if
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58 #end if
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59 #if $db_opts.db_opts_selector != "remote":
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60 -num_threads 8
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61 #end if
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62 #if $adv_opts.adv_opts_selector=="advanced":
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63 $adv_opts.filter_query
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64 -matrix $adv_opts.scoring.matrix
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65 $adv_opts.scoring.gap_costs
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66
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67 #if $adv_opts.word_size.__str__.strip() != '':
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68 -word_size $adv_opts.word_size
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69 #end if
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70
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71 #if $adv_opts.window_size.__str__.strip() != '':
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72 -window_size $adv_opts.window_size
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73 #end if
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74
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75 #if $adv_opts.threshold.__str__.strip() != '':
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76 -threshold $adv_opts.threshold
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77 #end if
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78
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79 #if $adv_opts.comp_based_stats.__str__.strip() != '':
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80 -comp_based_stats $adv_opts.comp_based_stats
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81 #end if
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82
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83 ##Ungapped disabled for now - see comments below
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84 ##$adv_opts.ungapped
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85 $adv_opts.use_sw_tback
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86 $adv_opts.parse_deflines
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87 ## End of advanced options:
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88 #end if
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89 </command>
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90 <inputs>
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91 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>
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92 <conditional name="db_opts">
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93 <param name="db_opts_selector" type="select" label="Subject database/sequences">
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94 <option value="db" selected="True">Local BLAST Database</option>
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95 <option value="file">Local FASTA file</option>
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96 <option value="remote">NCBI Remote Database</option>
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97 </param>
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98 <when value="db">
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99 <param name="database" type="select" label="Protein BLAST database">
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100 <options from_file="blastdb_p.loc">
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101 <column name="value" index="0"/>
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102 <column name="name" index="1"/>
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103 <column name="path" index="2"/>
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104 </options>
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105 </param>
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106 <param name="subject" type="hidden" value="" />
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107 </when>
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108 <when value="file">
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109 <param name="database" type="hidden" value="" />
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110 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/>
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111 </when>
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112 <when value="remote">
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113 <param name="database" type="select" label="Protein BLAST database">
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114 <option value="nr" selected="selected" >Non-redundant protein sequences (nr)</option>
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115 <option value="refseq_protein" >Reference proteins (refseq_protein)</option>
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116 <option value="swissprot" >UniProtKB/Swiss-Prot(swissprot)</option>
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117 <option value="pat" >Patented protein sequences(pat)</option>
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118 <option value="pdb" >Protein Data Bank proteins(pdb)</option>
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119 <option value="env_nr" >Metagenomic proteins(env_nr)</option>
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120 </param>
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121 <repeat name="taxid_repeat" title="Search Organism Restriction" min="0">
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122 <param name="taxid" type="integer" value="" label="NCBI Taxon ID" help="For example: Human is 9606 (see: http://www.ncbi.nlm.nih.gov/taxonomy ) ">
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123 <dsvalidator type="in_range" min="0" />
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124 </param>
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125 <param name="exclude" type="boolean" checked="false" label="Exclude this NCBI Taxon ID" help=""/>
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126 </repeat>
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127 </when>
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128 </conditional>
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129 <param name="blast_type" type="select" display="radio" label="Type of BLAST">
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130 <option value="blastp">blastp</option>
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131 <option value="blastp-short">blastp-short</option>
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132 </param>
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133 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
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134 <conditional name="fmt_opt">
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135 <param name="out_format" type="select" label="Output format">
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136 <option value="tabular" selected="True">Tabular</option>
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137 <option value="blastxml">BLAST XML</option>
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138 <option value="text">Text Report</option>
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139 </param>
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140 <when value="tabular">
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141 <param name="outfmt" type="select" label="Tabular columns">
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142 <option value="6" selected="True">Tabular (standard 12 columns)</option>
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143 <option value="7">Tabular (standard 12 columns) with comments</option>
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144 <option value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen">Tabular (extended 24 columns)</option>
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145 </param>
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146 <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits">
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147 <validator type="in_range" min="0" />
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148 </param>
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149 </when>
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150 <when value="blastxml">
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151 <param name="outfmt" type="hidden" value="5"/>
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152 <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits">
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153 <validator type="in_range" min="0" />
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154 </param>
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155 </when>
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156 <when value="text">
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157 <param name="outfmt" type="select" label="Text format">
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158 <option value="0">Pairwise text</option>
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159 <option value="1">Query-anchored text showing identitites</option>
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160 <option value="2">Query-anchored text</option>
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161 <option value="3">Flat query-anchored text showing identitites</option>
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162 <option value="4">Flat query-anchored text</option>
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163 </param>
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164 <param name="html" type="boolean" label="Html" truevalue="-html" falsevalue="" checked="true" />
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165 <param name="num_descriptions" type="integer" value="500" optional="true" label="Maximum Decriptions to show" help="Show one-line descriptions for this number of database sequences.">
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166 <validator type="in_range" min="0" />
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167 </param>
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168 <param name="num_alignments" type="integer" value="250" optional="true" label="Maximum alignments to show" help="Show alignments for this number of database sequences.">
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169 <validator type="in_range" min="0" />
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170 </param>
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171 </when>
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172 </conditional>
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173 <conditional name="adv_opts">
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174 <param name="adv_opts_selector" type="select" label="Advanced Options">
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175 <option value="basic" selected="True">Hide Advanced Options</option>
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176 <option value="advanced">Show Advanced Options</option>
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177 </param>
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178 <when value="basic" />
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179 <when value="advanced">
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180 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
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181 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
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182 <conditional name="scoring">
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183 <param name="matrix" type="select" label="Scoring matrix">
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184 <option value="BLOSUM90">BLOSUM90</option>
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185 <option value="BLOSUM80">BLOSUM80</option>
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186 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
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187 <option value="BLOSUM50">BLOSUM50</option>
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188 <option value="BLOSUM45">BLOSUM45</option>
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189 <option value="PAM250">PAM250</option>
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190 <option value="PAM70">PAM70</option>
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191 <option value="PAM30">PAM30</option>
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192 </param>
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193 <when value="BLOSUM90">
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194 <param name="gap_costs" type="select" label="Gap Costs">
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195 <option value="">Use Defaults</option>
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196 <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option>
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197 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
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198 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
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199 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
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200 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option>
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201 <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option>
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202 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
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203 </param>
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204
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205 </when>
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206 <when value="BLOSUM80">
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207 <param name="gap_costs" type="select" label="Gap Costs">
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208 <option value="">Use Defaults</option>
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209 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
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210 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
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211 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
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212 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option>
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213 <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option>
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214 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
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215 </param>
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216 </when>
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217 <when value="BLOSUM62">
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218 <param name="gap_costs" type="select" label="Gap Costs">
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219 <option value="">Use Defaults</option>
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220 <option value="-gapopen 11 -gapextend 2">Existense: 11 Extension: 2</option>
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221 <option value="-gapopen 10 -gapextend 2">Existense: 10 Extension: 2</option>
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222 <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option>
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223 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
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224 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
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225 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
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226 <option value="-gapopen 13 -gapextend 1">Existense: 13 Extension: 1</option>
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227 <option value="-gapopen 12 -gapextend 1">Existense: 12 Extension: 1</option>
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228 <option value="-gapopen 11 -gapextend 1" selected="true">Existense: 11 Extension: 1 (default)</option>
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229 <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option>
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230 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
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231 </param>
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232
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233 </when>
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234 <when value="BLOSUM50">
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235 <param name="gap_costs" type="select" label="Gap Costs">
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236 <option value="">Use Defaults</option>
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237 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option>
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238 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option>
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239 <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option>
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240 <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option>
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241 <option value="-gapopen 9 -gapextend 3">Existense: 9 Extension: 3</option>
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242 <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option>
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243 <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option>
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244 <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option>
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245 <option value="-gapopen 13 -gapextend 2" selected="true">Existense: 13 Extension: 2 (default)</option>
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246 <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option>
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247 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option>
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248 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option>
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249 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option>
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250 <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option>
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251 <option value="-gapopen 15 -gapextend 1">Existense: 15 Extension: 1</option>
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252 </param>
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253
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254 </when>
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255 <when value="BLOSUM45">
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256 <param name="gap_costs" type="select" label="Gap Costs">
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257 <option value="">Use Defaults</option>
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258 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option>
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259 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option>
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260 <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option>
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261 <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option>
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262 <option value="-gapopen 15 -gapextend 2" selected="true">Existense: 15 Extension: 2 (default)</option>
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263 <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option>
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264 <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option>
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265 <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option>
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266 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option>
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267 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option>
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268 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option>
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269 <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option>
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270 </param>
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271 </when>
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272 <when value="PAM250">
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273 <param name="gap_costs" type="select" label="Gap Costs">
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274 <option value="">Use Defaults</option>
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275 <option value="-gapopen 15 -gapextend 3">Existense: 15 Extension: 3</option>
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276 <option value="-gapopen 14 -gapextend 3">Existense: 14 Extension: 3</option>
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277 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option>
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278 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option>
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279 <option value="-gapopen 17 -gapextend 2">Existense: 17 Extension: 2</option>
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280 <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option>
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281 <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option>
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282 <option value="-gapopen 14 -gapextend 2" selected="true">Existense: 14 Extension: 2 (default)</option>
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283 <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option>
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284 <option value="-gapopen 21 -gapextend 1">Existense: 21 Extension: 1</option>
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285 <option value="-gapopen 20 -gapextend 1">Existense: 20 Extension: 1</option>
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286 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option>
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287 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option>
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288 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option>
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289 </param>
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290
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291 </when>
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292 <when value="PAM70">
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293 <param name="gap_costs" type="select" label="Gap Costs">
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294 <option value="">Use Defaults</option>
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295 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
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296 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
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297 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
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298 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option>
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299 <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option>
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300 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
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301 </param>
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302
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303 </when>
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304 <when value="PAM30">
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305 <param name="gap_costs" type="select" label="Gap Costs">
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306 <option value="">Use Defaults</option>
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307 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
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308 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
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309 <option value="-gapopen 5 -gapextend 2">Existense: 5 Extension: 2</option>
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310 <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option>
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311 <option value="-gapopen 9 -gapextend 1" selected="true">Existense: 9 Extension: 1 (default)</option>
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312 <option value="-gapopen 8 -gapextend 1">Existense: 8 Extension: 1</option>
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313 </param>
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314 </when>
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315 <!--
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316 Can't use '-ungapped' on its own, error back is:
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317 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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318 Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.'
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319 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
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320 -->
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321 </conditional>
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322
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323 <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
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324 <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2">
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325 <validator type="in_range" min="2" />
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326 </param>
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327 <param name="window_size" type="integer" value="" optional="true" label="Multiple hits window size, use 0 to specify 1-hit algorithm." help="Recommended: blastp 40, blastp-short 15">
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328 <validator type="in_range" min="0" />
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329 </param>
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330 <param name="threshold" type="integer" value="" optional="true" label="Threshold: Minimum score to add a word to the BLAST lookup table." help="Recommended: blastp 11, blastp-short 16">
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331 <validator type="in_range" min="1" />
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332 </param>
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333 <param name="comp_based_stats" type="select" optional="true" label="Use composition-based statistics"
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334 help="Recommended: blastp: 2 blastp-short: 0">
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335 <option value="">Leave Unspecified</option>
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336 <option value="0">0 or F (No composition-based statistics)</option>
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337 <option value="1">1 (Composition-based statistics as in NAR 29:2994-3005, 2001)</option>
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338 <option value="2">2, T, or D (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties)</option>
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339 <option value="3">3 (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally)</option>
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340 </param>
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341
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342 <param name="use_sw_tback" type="boolean" label="Compute locally optimal Smith-Waterman alignments?" truevalue="-use_sw_tback" falsevalue="" checked="false" />
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343
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344 <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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345 </when>
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346 </conditional>
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347 </inputs>
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348
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349 <outputs>
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350 <data name="output_tabular" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
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351 <filter>fmt_opt['out_format'] == "tabular"</filter>
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352 </data>
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353 <data name="output_xml" format="blastxml" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
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354 <filter>fmt_opt['out_format'] == "blastxml"</filter>
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355 </data>
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356 <data name="output_txt" format="txt" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
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357 <filter>fmt_opt['out_format'] == "text" and not fmt_opt['html']</filter>
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358 </data>
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359 <data name="output_html" format="html" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
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360 <filter>fmt_opt['out_format'] == "text" and fmt_opt['html']</filter>
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361 </data>
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362 </outputs>
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363
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364 <stdio>
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365 <exit_code range="1" level="fatal" description="Bad input dataset or BLAST options" />
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366 <exit_code range="2" level="fatal" description="Error in BLAST database" />
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367 <exit_code range="3" level="fatal" description="Error in BLAST engine" />
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368 <exit_code range="4" level="fatal" description="Out of Memory" />
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369 <exit_code range="5:" level="fatal" description="Unknown Error" />
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370 </stdio>
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371
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372 <tests>
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373 <test>
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374 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
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375 <param name="db_opts_selector" value="file" />
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376 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
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377 <param name="database" value="" />
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378 <param name="evalue_cutoff" value="1e-8" />
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379 <param name="blast_type" value="blastp" />
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380 <param name="out_format" value="blastxml" />
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381 <param name="outfmt" value="5" />
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382 <param name="adv_opts_selector" value="advanced" />
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383 <param name="filter_query" value="False" />
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384 <param name="matrix" value="BLOSUM62" />
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385 <param name="max_target_seqs" value="" />
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386 <param name="word_size" value="" />
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387 <param name="parse_deflines" value="True" />
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388 <output name="output_xml">
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389 <assert_contents>
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390 <has_text text="sp|Q9BS26|ERP44_HUMAN"/>
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391 </assert_contents>
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392 </output>
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393 </test>
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394 <test>
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395 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
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396 <param name="db_opts_selector" value="file" />
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397 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
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398 <param name="database" value="" />
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399 <param name="evalue_cutoff" value="1e-8" />
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400 <param name="blast_type" value="blastp" />
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401 <param name="out_format" value="tabular" />
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402 <param name="outfmt" value="6" />
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403 <param name="adv_opts_selector" value="advanced" />
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404 <param name="filter_query" value="False" />
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405 <param name="matrix" value="BLOSUM62" />
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406 <param name="max_target_seqs" value="" />
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407 <param name="word_size" value="" />
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408 <param name="parse_deflines" value="True" />
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409 <output name="output_tabular">
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410 <assert_contents>
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411 <has_text_matching expression="sp.P08100.OPSD_HUMAN\tgi.283855846.gb.ADB45242.1.\t\d+.\d+\t\d+\t\d+\t0\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+" />
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412 <has_text text="BAB21486.1"/>
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413 </assert_contents>
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414 </output>
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415 </test>
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416 <test>
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417 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
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418 <param name="db_opts_selector" value="file" />
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419 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
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420 <param name="database" value="" />
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421 <param name="evalue_cutoff" value="1e-8" />
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422 <param name="blast_type" value="blastp" />
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423 <param name="out_format" value="tabular" />
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|
424 <param name="outfmt" value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" />
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425 <param name="adv_opts_selector" value="advanced" />
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|
426 <param name="filter_query" value="False" />
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|
427 <param name="matrix" value="BLOSUM62" />
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|
428 <param name="max_target_seqs" value="" />
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|
|
429 <param name="word_size" value="" />
|
|
|
430 <param name="parse_deflines" value="True" />
|
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|
431 <output name="output_tabular">
|
|
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432 <assert_contents>
|
|
|
433 <has_text_matching expression="sp.P08100.OPSD_HUMAN\tgi.283855846.gb.ADB45242.1.\t\d+.\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+\t\S+\t\d+\t\d+\t\d+\t\d+\t\S+\t\d+\t\d+\t\S+\t\S+\t\d+\t\d+" />
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434 </assert_contents>
|
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435 </output>
|
|
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436 </test>
|
|
|
437 <test>
|
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|
438 <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />
|
|
|
439 <param name="db_opts_selector" value="file" />
|
|
|
440 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
|
|
|
441 <param name="database" value="" />
|
|
|
442 <param name="evalue_cutoff" value="1e-8" />
|
|
|
443 <param name="blast_type" value="blastp" />
|
|
|
444 <param name="out_format" value="tabular" />
|
|
|
445 <param name="outfmt" value="6" />
|
|
|
446 <param name="adv_opts_selector" value="basic" />
|
|
|
447 <output name="output_tabular">
|
|
|
448 <assert_contents>
|
|
|
449 <has_text_matching expression="gi.283855846.gb.ADB45242.1.\tsp.P08100.OPSD_HUMAN\t\d+.\d+\t\d+\t\d+\t0\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+" />
|
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450 <has_text text="BAB21486.1"/>
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|
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451 </assert_contents>
|
|
|
452 </output>
|
|
|
453 </test>
|
|
|
454 </tests>
|
|
|
455 <help>
|
|
|
456
|
|
|
457 .. class:: warningmark
|
|
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458
|
|
|
459 **Note**. Database searches may take a substantial amount of time.
|
|
|
460 For large input datasets it is advisable to allow overnight processing.
|
|
|
461
|
|
|
462 -----
|
|
|
463
|
|
|
464 **What it does**
|
|
|
465
|
|
|
466 Search a *protein database* using a *protein query*,
|
|
|
467 using the NCBI BLAST+ blastp command line tool.
|
|
|
468
|
|
|
469 The search can be performed using a local database, against a sequence supplied in a fasta file,
|
|
|
470 or the blast can be performed remotely at NCBI.
|
|
|
471
|
|
|
472 The remote operation allows searches to be targeted at specific organisms.
|
|
|
473
|
|
|
474 -----
|
|
|
475
|
|
|
476 **Output format**
|
|
|
477
|
|
|
478 Because Galaxy focuses on processing tabular data, the default output of this
|
|
|
479 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
|
|
|
480
|
|
|
481 ====== ========= ============================================
|
|
|
482 Column NCBI name Description
|
|
|
483 ------ --------- --------------------------------------------
|
|
|
484 1 qseqid Query Seq-id (ID of your sequence)
|
|
|
485 2 sseqid Subject Seq-id (ID of the database hit)
|
|
|
486 3 pident Percentage of identical matches
|
|
|
487 4 length Alignment length
|
|
|
488 5 mismatch Number of mismatches
|
|
|
489 6 gapopen Number of gap openings
|
|
|
490 7 qstart Start of alignment in query
|
|
|
491 8 qend End of alignment in query
|
|
|
492 9 sstart Start of alignment in subject (database hit)
|
|
|
493 10 send End of alignment in subject (database hit)
|
|
|
494 11 evalue Expectation value (E-value)
|
|
|
495 12 bitscore Bit score
|
|
|
496 ====== ========= ============================================
|
|
|
497
|
|
|
498 The BLAST+ tools can optionally output additional columns of information,
|
|
|
499 but this takes longer to calculate. Most (but not all) of these columns are
|
|
|
500 included by selecting the extended tabular output. The extra columns are
|
|
|
501 included *after* the standard 12 columns. This is so that you can write
|
|
|
502 workflow filtering steps that accept either the 12 or 24 column tabular
|
|
|
503 BLAST output.
|
|
|
504
|
|
|
505 ====== ============= ===========================================
|
|
|
506 Column NCBI name Description
|
|
|
507 ------ ------------- -------------------------------------------
|
|
|
508 13 sallseqid All subject Seq-id(s), separated by a ';'
|
|
|
509 14 score Raw score
|
|
|
510 15 nident Number of identical matches
|
|
|
511 16 positive Number of positive-scoring matches
|
|
|
512 17 gaps Total number of gaps
|
|
|
513 18 ppos Percentage of positive-scoring matches
|
|
|
514 19 qframe Query frame
|
|
|
515 20 sframe Subject frame
|
|
|
516 21 qseq Aligned part of query sequence
|
|
|
517 22 sseq Aligned part of subject sequence
|
|
|
518 23 qlen Query sequence length
|
|
|
519 24 slen Subject sequence length
|
|
|
520 ====== ============= ===========================================
|
|
|
521
|
|
|
522 The third option is BLAST XML output, which is designed to be parsed by
|
|
|
523 another program, and is understood by some Galaxy tools.
|
|
|
524
|
|
|
525 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
|
|
|
526 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
|
|
|
527 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
|
|
|
528 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
|
|
|
529 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
|
|
|
530
|
|
|
531 -------
|
|
|
532
|
|
|
533 **References**
|
|
|
534
|
|
|
535 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
|
|
|
536
|
|
|
537 Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005.
|
|
|
538
|
|
|
539 </help>
|
|
|
540 </tool>
|
