annotate tools/blast_plus_remote_blastp.xml @ 3:9f369b905447

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author galaxyp
date Wed, 01 Oct 2014 21:08:57 -0400
parents db990c5edc14
children a51980bc0ffe
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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 <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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4 <version_command>blastp -version</version_command>
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5 <requirements>
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6 <requirement type="binary">blastp</requirement>
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7 <requirement type="package" version="2.2.29">blast+</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 <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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181 <conditional name="scoring">
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182 <param name="matrix" type="select" label="Scoring matrix">
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183 <option value="BLOSUM90">BLOSUM90</option>
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184 <option value="BLOSUM80">BLOSUM80</option>
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185 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
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186 <option value="BLOSUM50">BLOSUM50</option>
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187 <option value="BLOSUM45">BLOSUM45</option>
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188 <option value="PAM250">PAM250</option>
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189 <option value="PAM70">PAM70</option>
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190 <option value="PAM30">PAM30</option>
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191 </param>
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192 <when value="BLOSUM90">
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193 <param name="gap_costs" type="select" label="Gap Costs">
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194 <option value="">Use Defaults</option>
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195 <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option>
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196 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
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197 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
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198 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
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199 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
200 <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
201 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
202 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
203
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
204 </when>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
205 <when value="BLOSUM80">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
206 <param name="gap_costs" type="select" label="Gap Costs">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
207 <option value="">Use Defaults</option>
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galaxyp
parents:
diff changeset
208 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
209 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
210 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
211 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
212 <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option>
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galaxyp
parents:
diff changeset
213 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
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galaxyp
parents:
diff changeset
214 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
215 </when>
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galaxyp
parents:
diff changeset
216 <when value="BLOSUM62">
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galaxyp
parents:
diff changeset
217 <param name="gap_costs" type="select" label="Gap Costs">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
218 <option value="">Use Defaults</option>
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galaxyp
parents:
diff changeset
219 <option value="-gapopen 11 -gapextend 2">Existense: 11 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
220 <option value="-gapopen 10 -gapextend 2">Existense: 10 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
221 <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
222 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
223 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
224 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
225 <option value="-gapopen 13 -gapextend 1">Existense: 13 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
226 <option value="-gapopen 12 -gapextend 1">Existense: 12 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
227 <option value="-gapopen 11 -gapextend 1" selected="true">Existense: 11 Extension: 1 (default)</option>
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galaxyp
parents:
diff changeset
228 <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
229 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
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galaxyp
parents:
diff changeset
230 </param>
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galaxyp
parents:
diff changeset
231
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
232 </when>
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galaxyp
parents:
diff changeset
233 <when value="BLOSUM50">
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galaxyp
parents:
diff changeset
234 <param name="gap_costs" type="select" label="Gap Costs">
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galaxyp
parents:
diff changeset
235 <option value="">Use Defaults</option>
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galaxyp
parents:
diff changeset
236 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
237 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
238 <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
239 <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
240 <option value="-gapopen 9 -gapextend 3">Existense: 9 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
241 <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
242 <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
243 <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
244 <option value="-gapopen 13 -gapextend 2" selected="true">Existense: 13 Extension: 2 (default)</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
245 <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
246 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
247 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
248 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
249 <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
250 <option value="-gapopen 15 -gapextend 1">Existense: 15 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
251 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
252
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
253 </when>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
254 <when value="BLOSUM45">
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galaxyp
parents:
diff changeset
255 <param name="gap_costs" type="select" label="Gap Costs">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
256 <option value="">Use Defaults</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
257 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
258 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
259 <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
260 <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
261 <option value="-gapopen 15 -gapextend 2" selected="true">Existense: 15 Extension: 2 (default)</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
262 <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
263 <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
264 <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
265 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
266 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
267 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
268 <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option>
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galaxyp
parents:
diff changeset
269 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
270 </when>
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galaxyp
parents:
diff changeset
271 <when value="PAM250">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
272 <param name="gap_costs" type="select" label="Gap Costs">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
273 <option value="">Use Defaults</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
274 <option value="-gapopen 15 -gapextend 3">Existense: 15 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
275 <option value="-gapopen 14 -gapextend 3">Existense: 14 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
276 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
277 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
278 <option value="-gapopen 17 -gapextend 2">Existense: 17 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
279 <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
280 <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
281 <option value="-gapopen 14 -gapextend 2" selected="true">Existense: 14 Extension: 2 (default)</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
282 <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
283 <option value="-gapopen 21 -gapextend 1">Existense: 21 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
284 <option value="-gapopen 20 -gapextend 1">Existense: 20 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
285 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
286 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
287 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
288 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
289
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
290 </when>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
291 <when value="PAM70">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
292 <param name="gap_costs" type="select" label="Gap Costs">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
293 <option value="">Use Defaults</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
294 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
295 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
296 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
297 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
298 <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
299 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
300 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
301
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
302 </when>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
303 <when value="PAM30">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
304 <param name="gap_costs" type="select" label="Gap Costs">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
305 <option value="">Use Defaults</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
306 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
307 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
308 <option value="-gapopen 5 -gapextend 2">Existense: 5 Extension: 2</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
309 <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
310 <option value="-gapopen 9 -gapextend 1" selected="true">Existense: 9 Extension: 1 (default)</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
311 <option value="-gapopen 8 -gapextend 1">Existense: 8 Extension: 1</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
312 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
313 </when>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
314 </conditional>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
315
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
316 <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
317 <validator type="in_range" min="2" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
318 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
319 <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">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
320 <validator type="in_range" min="0" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
321 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
322 <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">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
323 <validator type="in_range" min="1" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
324 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
325 <param name="comp_based_stats" type="select" optional="true" label="Use composition-based statistics"
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
326 help="Recommended: blastp: 2 blastp-short: 0">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
327 <option value="">Leave Unspecified</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
328 <option value="0">0 or F (No composition-based statistics)</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
329 <option value="1">1 (Composition-based statistics as in NAR 29:2994-3005, 2001)</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
330 <option value="2">2, T, or D (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties)</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
331 <option value="3">3 (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally)</option>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
332 </param>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
333
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
334 <param name="use_sw_tback" type="boolean" label="Compute locally optimal Smith-Waterman alignments?" truevalue="-use_sw_tback" falsevalue="" checked="false" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
335
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
336 <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"/>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
337 </when>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
338 </conditional>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
339 </inputs>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
340
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
341 <outputs>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
342 <data name="output_tabular" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
343 <filter>fmt_opt['out_format'] == "tabular"</filter>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
344 </data>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
345 <data name="output_xml" format="blastxml" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
346 <filter>fmt_opt['out_format'] == "blastxml"</filter>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
347 </data>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
348 <data name="output_txt" format="txt" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
349 <filter>fmt_opt['out_format'] == "text" and not fmt_opt['html']</filter>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
350 </data>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
351 <data name="output_html" format="html" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
352 <filter>fmt_opt['out_format'] == "text" and fmt_opt['html']</filter>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
353 </data>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
354 </outputs>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
355
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
356 <stdio>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
357 <exit_code range="1" level="fatal" description="Bad input dataset or BLAST options" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
358 <exit_code range="2" level="fatal" description="Error in BLAST database" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
359 <exit_code range="3" level="fatal" description="Error in BLAST engine" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
360 <exit_code range="4" level="fatal" description="Out of Memory" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
361 <exit_code range="5:" level="fatal" description="Unknown Error" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
362 </stdio>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
363
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
364 <tests>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
365 <test>
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
366 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
367 <param name="db_opts_selector" value="file" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
368 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
369 <param name="database" value="" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
370 <param name="evalue_cutoff" value="1e-8" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
371 <param name="blast_type" value="blastp" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
372 <param name="out_format" value="blastxml" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
373 <param name="outfmt" value="5" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
374 <param name="adv_opts_selector" value="advanced" />
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
375 <param name="filter_query" value="False" />
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galaxyp
parents:
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376 <param name="matrix" value="BLOSUM62" />
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galaxyp
parents:
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377 <param name="max_target_seqs" value="" />
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galaxyp
parents:
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378 <param name="word_size" value="" />
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galaxyp
parents:
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379 <param name="parse_deflines" value="True" />
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galaxyp
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380 <output name="output_xml">
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galaxyp
parents:
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381 <assert_contents>
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galaxyp
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382 <has_text text="sp|Q9BS26|ERP44_HUMAN"/>
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galaxyp
parents:
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383 </assert_contents>
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galaxyp
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384 </output>
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galaxyp
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385 </test>
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galaxyp
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386 <test>
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galaxyp
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387 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
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galaxyp
parents:
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388 <param name="db_opts_selector" value="file" />
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galaxyp
parents:
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389 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
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galaxyp
parents:
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390 <param name="database" value="" />
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galaxyp
parents:
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391 <param name="evalue_cutoff" value="1e-8" />
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galaxyp
parents:
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392 <param name="blast_type" value="blastp" />
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galaxyp
parents:
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393 <param name="out_format" value="tabular" />
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galaxyp
parents:
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394 <param name="outfmt" value="6" />
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galaxyp
parents:
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395 <param name="adv_opts_selector" value="advanced" />
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galaxyp
parents:
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396 <param name="filter_query" value="False" />
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galaxyp
parents:
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397 <param name="matrix" value="BLOSUM62" />
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galaxyp
parents:
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398 <param name="max_target_seqs" value="" />
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galaxyp
parents:
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399 <param name="word_size" value="" />
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galaxyp
parents:
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400 <param name="parse_deflines" value="True" />
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galaxyp
parents:
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401 <output name="output_tabular">
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galaxyp
parents:
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402 <assert_contents>
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galaxyp
parents:
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403 <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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galaxyp
parents:
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404 <has_text text="BAB21486.1"/>
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galaxyp
parents:
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405 </assert_contents>
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galaxyp
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406 </output>
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galaxyp
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407 </test>
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galaxyp
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408 <test>
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galaxyp
parents:
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409 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
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galaxyp
parents:
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410 <param name="db_opts_selector" value="file" />
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galaxyp
parents:
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411 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
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galaxyp
parents:
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412 <param name="database" value="" />
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galaxyp
parents:
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413 <param name="evalue_cutoff" value="1e-8" />
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galaxyp
parents:
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414 <param name="blast_type" value="blastp" />
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galaxyp
parents:
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415 <param name="out_format" value="tabular" />
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galaxyp
parents:
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416 <param name="outfmt" value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" />
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galaxyp
parents:
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417 <param name="adv_opts_selector" value="advanced" />
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galaxyp
parents:
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418 <param name="filter_query" value="False" />
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galaxyp
parents:
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419 <param name="matrix" value="BLOSUM62" />
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galaxyp
parents:
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420 <param name="max_target_seqs" value="" />
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galaxyp
parents:
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421 <param name="word_size" value="" />
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galaxyp
parents:
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422 <param name="parse_deflines" value="True" />
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galaxyp
parents:
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423 <output name="output_tabular">
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galaxyp
parents:
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424 <assert_contents>
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galaxyp
parents:
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425 <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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galaxyp
parents:
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426 </assert_contents>
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galaxyp
parents:
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427 </output>
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galaxyp
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428 </test>
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galaxyp
parents:
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429 <test>
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galaxyp
parents:
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430 <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />
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galaxyp
parents:
diff changeset
431 <param name="db_opts_selector" value="file" />
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galaxyp
parents:
diff changeset
432 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
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galaxyp
parents:
diff changeset
433 <param name="database" value="" />
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galaxyp
parents:
diff changeset
434 <param name="evalue_cutoff" value="1e-8" />
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galaxyp
parents:
diff changeset
435 <param name="blast_type" value="blastp" />
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galaxyp
parents:
diff changeset
436 <param name="out_format" value="tabular" />
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galaxyp
parents:
diff changeset
437 <param name="outfmt" value="6" />
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galaxyp
parents:
diff changeset
438 <param name="adv_opts_selector" value="basic" />
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galaxyp
parents:
diff changeset
439 <output name="output_tabular">
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galaxyp
parents:
diff changeset
440 <assert_contents>
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galaxyp
parents:
diff changeset
441 <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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galaxyp
parents:
diff changeset
442 <has_text text="BAB21486.1"/>
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galaxyp
parents:
diff changeset
443 </assert_contents>
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galaxyp
parents:
diff changeset
444 </output>
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galaxyp
parents:
diff changeset
445 </test>
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galaxyp
parents:
diff changeset
446 </tests>
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galaxyp
parents:
diff changeset
447 <help>
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galaxyp
parents:
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448
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galaxyp
parents:
diff changeset
449 .. class:: warningmark
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galaxyp
parents:
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450
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galaxyp
parents:
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451 **Note**. Database searches may take a substantial amount of time.
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galaxyp
parents:
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452 For large input datasets it is advisable to allow overnight processing.
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galaxyp
parents:
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453
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galaxyp
parents:
diff changeset
454 -----
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galaxyp
parents:
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455
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galaxyp
parents:
diff changeset
456 **What it does**
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galaxyp
parents:
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457
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galaxyp
parents:
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458 Search a *protein database* using a *protein query*,
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galaxyp
parents:
diff changeset
459 using the NCBI BLAST+ blastp command line tool.
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galaxyp
parents:
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460
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galaxyp
parents:
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461 The search can be performed using a local database, against a sequence supplied in a fasta file,
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galaxyp
parents:
diff changeset
462 or the blast can be performed remotely at NCBI.
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galaxyp
parents:
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463
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galaxyp
parents:
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464 The remote operation allows searches to be targeted at specific organisms.
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galaxyp
parents:
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465
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galaxyp
parents:
diff changeset
466 -----
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galaxyp
parents:
diff changeset
467
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galaxyp
parents:
diff changeset
468 **Output format**
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galaxyp
parents:
diff changeset
469
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galaxyp
parents:
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470 Because Galaxy focuses on processing tabular data, the default output of this
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galaxyp
parents:
diff changeset
471 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
472
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galaxyp
parents:
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473 ====== ========= ============================================
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galaxyp
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diff changeset
474 Column NCBI name Description
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galaxyp
parents:
diff changeset
475 ------ --------- --------------------------------------------
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galaxyp
parents:
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476 1 qseqid Query Seq-id (ID of your sequence)
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galaxyp
parents:
diff changeset
477 2 sseqid Subject Seq-id (ID of the database hit)
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galaxyp
parents:
diff changeset
478 3 pident Percentage of identical matches
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galaxyp
parents:
diff changeset
479 4 length Alignment length
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galaxyp
parents:
diff changeset
480 5 mismatch Number of mismatches
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galaxyp
parents:
diff changeset
481 6 gapopen Number of gap openings
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galaxyp
parents:
diff changeset
482 7 qstart Start of alignment in query
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galaxyp
parents:
diff changeset
483 8 qend End of alignment in query
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galaxyp
parents:
diff changeset
484 9 sstart Start of alignment in subject (database hit)
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galaxyp
parents:
diff changeset
485 10 send End of alignment in subject (database hit)
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galaxyp
parents:
diff changeset
486 11 evalue Expectation value (E-value)
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galaxyp
parents:
diff changeset
487 12 bitscore Bit score
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galaxyp
parents:
diff changeset
488 ====== ========= ============================================
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galaxyp
parents:
diff changeset
489
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galaxyp
parents:
diff changeset
490 The BLAST+ tools can optionally output additional columns of information,
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galaxyp
parents:
diff changeset
491 but this takes longer to calculate. Most (but not all) of these columns are
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galaxyp
parents:
diff changeset
492 included by selecting the extended tabular output. The extra columns are
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
493 included *after* the standard 12 columns. This is so that you can write
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galaxyp
parents:
diff changeset
494 workflow filtering steps that accept either the 12 or 24 column tabular
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
495 BLAST output.
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galaxyp
parents:
diff changeset
496
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
497 ====== ============= ===========================================
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galaxyp
parents:
diff changeset
498 Column NCBI name Description
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galaxyp
parents:
diff changeset
499 ------ ------------- -------------------------------------------
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galaxyp
parents:
diff changeset
500 13 sallseqid All subject Seq-id(s), separated by a ';'
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galaxyp
parents:
diff changeset
501 14 score Raw score
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galaxyp
parents:
diff changeset
502 15 nident Number of identical matches
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galaxyp
parents:
diff changeset
503 16 positive Number of positive-scoring matches
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galaxyp
parents:
diff changeset
504 17 gaps Total number of gaps
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galaxyp
parents:
diff changeset
505 18 ppos Percentage of positive-scoring matches
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galaxyp
parents:
diff changeset
506 19 qframe Query frame
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galaxyp
parents:
diff changeset
507 20 sframe Subject frame
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galaxyp
parents:
diff changeset
508 21 qseq Aligned part of query sequence
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galaxyp
parents:
diff changeset
509 22 sseq Aligned part of subject sequence
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galaxyp
parents:
diff changeset
510 23 qlen Query sequence length
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galaxyp
parents:
diff changeset
511 24 slen Subject sequence length
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galaxyp
parents:
diff changeset
512 ====== ============= ===========================================
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galaxyp
parents:
diff changeset
513
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galaxyp
parents:
diff changeset
514 The third option is BLAST XML output, which is designed to be parsed by
820c41bff462 Uploaded
galaxyp
parents:
diff changeset
515 another program, and is understood by some Galaxy tools.
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galaxyp
parents:
diff changeset
516
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galaxyp
parents:
diff changeset
517 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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galaxyp
parents:
diff changeset
518 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
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galaxyp
parents:
diff changeset
519 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
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galaxyp
parents:
diff changeset
520 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
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galaxyp
parents:
diff changeset
521 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
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galaxyp
parents:
diff changeset
522
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galaxyp
parents:
diff changeset
523 -------
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galaxyp
parents:
diff changeset
524
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galaxyp
parents:
diff changeset
525 **References**
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galaxyp
parents:
diff changeset
526
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galaxyp
parents:
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527 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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galaxyp
parents:
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528
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galaxyp
parents:
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529 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.
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galaxyp
parents:
diff changeset
530
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galaxyp
parents:
diff changeset
531 </help>
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galaxyp
parents:
diff changeset
532 </tool>