Mercurial > repos > galaxyp > blast_plus_remote_blastp
comparison tools/blast_plus_remote_blastp.xml @ 0:820c41bff462
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| author | galaxyp |
|---|---|
| date | Wed, 01 Oct 2014 20:47:55 -0400 |
| parents | |
| children | db990c5edc14 |
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| -1:000000000000 | 0:820c41bff462 |
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| 1 <tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0"> | |
| 2 <description>Search protein database with protein query sequence(s)</description> | |
| 3 <!-- If job splitting is enabled, break up the query file into four (This only works if output is tabular) --> | |
| 4 <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism> | |
| 5 <version_command>blastp -version</version_command> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="333">binaries_for_blast_plus</requirement> | |
| 8 </requirements> | |
| 9 <command> | |
| 10 ## The command is a Cheetah template which allows some Python based syntax. | |
| 11 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces | |
| 12 blastp | |
| 13 -query "$query" | |
| 14 #if $db_opts.db_opts_selector == "db": | |
| 15 -db "${db_opts.database.fields.path}" | |
| 16 #elif $db_opts.db_opts_selector == "remote": | |
| 17 -db $db_opts.database | |
| 18 -remote | |
| 19 #set $txids = [] | |
| 20 #set $ntxids = [] | |
| 21 #for $i, $org in enumerate($db_opts.taxid_repeat): | |
| 22 #if $org.exclude: | |
| 23 #set $ntxids = $ntxids + ["txid" + $org.taxid.__str__] | |
| 24 #else | |
| 25 #set $txids = $txids + ["txid" + $org.taxid.__str__] | |
| 26 #end if | |
| 27 #end for | |
| 28 #if (len($txids) + len($ntxids)) > 0: | |
| 29 #set $entrez_query = '' | |
| 30 #if len($txids) > 0: | |
| 31 #set $entrez_query = $entrez_query + '(' + ' OR '.join($txids) + ')' | |
| 32 #end if | |
| 33 #if len($ntxids) > 0: | |
| 34 #set $entrez_query = $entrez_query + ' NOT (' + ' OR '.join($ntxids) + ')' | |
| 35 #end if | |
| 36 -entrez_query '$entrez_query' | |
| 37 #end if | |
| 38 #else: | |
| 39 -subject "$db_opts.subject" | |
| 40 #end if | |
| 41 -task $blast_type | |
| 42 -evalue $evalue_cutoff | |
| 43 -out blast_output | |
| 44 ##Set the extended list here so if/when we add things, saved workflows are not affected | |
| 45 #if str($fmt_opt.out_format)=="text": | |
| 46 -outfmt "$fmt_opt.outfmt" $fmt_opt.html | |
| 47 #if $fmt_opt.num_descriptions.__str__.strip() != '': | |
| 48 -num_descriptions $fmt_opt.num_descriptions | |
| 49 #end if | |
| 50 #if $fmt_opt.num_alignments.__str__.strip() != '': | |
| 51 -num_alignments $fmt_opt.num_alignments | |
| 52 #end if | |
| 53 #else: | |
| 54 -outfmt "$fmt_opt.outfmt" | |
| 55 #if $fmt_opt.max_target_seqs.__str__.strip() != '': | |
| 56 -max_target_seqs $fmt_opt.max_target_seqs | |
| 57 #end if | |
| 58 #end if | |
| 59 #if $db_opts.db_opts_selector != "remote": | |
| 60 -num_threads 8 | |
| 61 #end if | |
| 62 #if $adv_opts.adv_opts_selector=="advanced": | |
| 63 $adv_opts.filter_query | |
| 64 -matrix $adv_opts.scoring.matrix | |
| 65 $adv_opts.scoring.gap_costs | |
| 66 | |
| 67 #if $adv_opts.word_size.__str__.strip() != '': | |
| 68 -word_size $adv_opts.word_size | |
| 69 #end if | |
| 70 | |
| 71 #if $adv_opts.window_size.__str__.strip() != '': | |
| 72 -window_size $adv_opts.window_size | |
| 73 #end if | |
| 74 | |
| 75 #if $adv_opts.threshold.__str__.strip() != '': | |
| 76 -threshold $adv_opts.threshold | |
| 77 #end if | |
| 78 | |
| 79 #if $adv_opts.comp_based_stats.__str__.strip() != '': | |
| 80 -comp_based_stats $adv_opts.comp_based_stats | |
| 81 #end if | |
| 82 | |
| 83 ##Ungapped disabled for now - see comments below | |
| 84 ##$adv_opts.ungapped | |
| 85 $adv_opts.use_sw_tback | |
| 86 $adv_opts.parse_deflines | |
| 87 ## End of advanced options: | |
| 88 #end if | |
| 89 </command> | |
| 90 <inputs> | |
| 91 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> | |
| 92 <conditional name="db_opts"> | |
| 93 <param name="db_opts_selector" type="select" label="Subject database/sequences"> | |
| 94 <option value="db" selected="True">Local BLAST Database</option> | |
| 95 <option value="file">Local FASTA file</option> | |
| 96 <option value="remote">NCBI Remote Database</option> | |
| 97 </param> | |
| 98 <when value="db"> | |
| 99 <param name="database" type="select" label="Protein BLAST database"> | |
| 100 <options from_file="blastdb_p.loc"> | |
| 101 <column name="value" index="0"/> | |
| 102 <column name="name" index="1"/> | |
| 103 <column name="path" index="2"/> | |
| 104 </options> | |
| 105 </param> | |
| 106 <param name="subject" type="hidden" value="" /> | |
| 107 </when> | |
| 108 <when value="file"> | |
| 109 <param name="database" type="hidden" value="" /> | |
| 110 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> | |
| 111 </when> | |
| 112 <when value="remote"> | |
| 113 <param name="database" type="select" label="Protein BLAST database"> | |
| 114 <option value="nr" selected="selected" >Non-redundant protein sequences (nr)</option> | |
| 115 <option value="refseq_protein" >Reference proteins (refseq_protein)</option> | |
| 116 <option value="swissprot" >UniProtKB/Swiss-Prot(swissprot)</option> | |
| 117 <option value="pat" >Patented protein sequences(pat)</option> | |
| 118 <option value="pdb" >Protein Data Bank proteins(pdb)</option> | |
| 119 <option value="env_nr" >Metagenomic proteins(env_nr)</option> | |
| 120 </param> | |
| 121 <repeat name="taxid_repeat" title="Search Organism Restriction" min="0"> | |
| 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 ) "> | |
| 123 <dsvalidator type="in_range" min="0" /> | |
| 124 </param> | |
| 125 <param name="exclude" type="boolean" checked="false" label="Exclude this NCBI Taxon ID" help=""/> | |
| 126 </repeat> | |
| 127 </when> | |
| 128 </conditional> | |
| 129 <param name="blast_type" type="select" display="radio" label="Type of BLAST"> | |
| 130 <option value="blastp">blastp</option> | |
| 131 <option value="blastp-short">blastp-short</option> | |
| 132 </param> | |
| 133 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> | |
| 134 <conditional name="fmt_opt"> | |
| 135 <param name="out_format" type="select" label="Output format"> | |
| 136 <option value="tabular" selected="True">Tabular</option> | |
| 137 <option value="blastxml">BLAST XML</option> | |
| 138 <option value="text">Text Report</option> | |
| 139 </param> | |
| 140 <when value="tabular"> | |
| 141 <param name="outfmt" type="select" label="Tabular columns"> | |
| 142 <option value="6" selected="True">Tabular (standard 12 columns)</option> | |
| 143 <option value="7">Tabular (standard 12 columns) with comments</option> | |
| 144 <option value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen">Tabular (extended 24 columns)</option> | |
| 145 </param> | |
| 146 <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits"> | |
| 147 <validator type="in_range" min="0" /> | |
| 148 </param> | |
| 149 </when> | |
| 150 <when value="blastxml"> | |
| 151 <param name="outfmt" type="hidden" value="5"/> | |
| 152 <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits"> | |
| 153 <validator type="in_range" min="0" /> | |
| 154 </param> | |
| 155 </when> | |
| 156 <when value="text"> | |
| 157 <param name="outfmt" type="select" label="Text format"> | |
| 158 <option value="0">Pairwise text</option> | |
| 159 <option value="1">Query-anchored text showing identitites</option> | |
| 160 <option value="2">Query-anchored text</option> | |
| 161 <option value="3">Flat query-anchored text showing identitites</option> | |
| 162 <option value="4">Flat query-anchored text</option> | |
| 163 </param> | |
| 164 <param name="html" type="boolean" label="Html" truevalue="-html" falsevalue="" checked="true" /> | |
| 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."> | |
| 166 <validator type="in_range" min="0" /> | |
| 167 </param> | |
| 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."> | |
| 169 <validator type="in_range" min="0" /> | |
| 170 </param> | |
| 171 </when> | |
| 172 </conditional> | |
| 173 <conditional name="adv_opts"> | |
| 174 <param name="adv_opts_selector" type="select" label="Advanced Options"> | |
| 175 <option value="basic" selected="True">Hide Advanced Options</option> | |
| 176 <option value="advanced">Show Advanced Options</option> | |
| 177 </param> | |
| 178 <when value="basic" /> | |
| 179 <when value="advanced"> | |
| 180 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> | |
| 181 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> | |
| 182 <conditional name="scoring"> | |
| 183 <param name="matrix" type="select" label="Scoring matrix"> | |
| 184 <option value="BLOSUM90">BLOSUM90</option> | |
| 185 <option value="BLOSUM80">BLOSUM80</option> | |
| 186 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> | |
| 187 <option value="BLOSUM50">BLOSUM50</option> | |
| 188 <option value="BLOSUM45">BLOSUM45</option> | |
| 189 <option value="PAM250">PAM250</option> | |
| 190 <option value="PAM70">PAM70</option> | |
| 191 <option value="PAM30">PAM30</option> | |
| 192 </param> | |
| 193 <when value="BLOSUM90"> | |
| 194 <param name="gap_costs" type="select" label="Gap Costs"> | |
| 195 <option value="">Use Defaults</option> | |
| 196 <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option> | |
| 197 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> | |
| 198 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> | |
| 199 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> | |
| 200 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option> | |
| 201 <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option> | |
| 202 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> | |
| 203 </param> | |
| 204 | |
| 205 </when> | |
| 206 <when value="BLOSUM80"> | |
| 207 <param name="gap_costs" type="select" label="Gap Costs"> | |
| 208 <option value="">Use Defaults</option> | |
| 209 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> | |
| 210 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> | |
| 211 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> | |
| 212 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option> | |
| 213 <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option> | |
| 214 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> | |
| 215 </param> | |
| 216 </when> | |
| 217 <when value="BLOSUM62"> | |
| 218 <param name="gap_costs" type="select" label="Gap Costs"> | |
| 219 <option value="">Use Defaults</option> | |
| 220 <option value="-gapopen 11 -gapextend 2">Existense: 11 Extension: 2</option> | |
| 221 <option value="-gapopen 10 -gapextend 2">Existense: 10 Extension: 2</option> | |
| 222 <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option> | |
| 223 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> | |
| 224 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> | |
| 225 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> | |
| 226 <option value="-gapopen 13 -gapextend 1">Existense: 13 Extension: 1</option> | |
| 227 <option value="-gapopen 12 -gapextend 1">Existense: 12 Extension: 1</option> | |
| 228 <option value="-gapopen 11 -gapextend 1" selected="true">Existense: 11 Extension: 1 (default)</option> | |
| 229 <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option> | |
| 230 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> | |
| 231 </param> | |
| 232 | |
| 233 </when> | |
| 234 <when value="BLOSUM50"> | |
| 235 <param name="gap_costs" type="select" label="Gap Costs"> | |
| 236 <option value="">Use Defaults</option> | |
| 237 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option> | |
| 238 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option> | |
| 239 <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option> | |
| 240 <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option> | |
| 241 <option value="-gapopen 9 -gapextend 3">Existense: 9 Extension: 3</option> | |
| 242 <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option> | |
| 243 <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option> | |
| 244 <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option> | |
| 245 <option value="-gapopen 13 -gapextend 2" selected="true">Existense: 13 Extension: 2 (default)</option> | |
| 246 <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option> | |
| 247 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option> | |
| 248 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option> | |
| 249 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option> | |
| 250 <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option> | |
| 251 <option value="-gapopen 15 -gapextend 1">Existense: 15 Extension: 1</option> | |
| 252 </param> | |
| 253 | |
| 254 </when> | |
| 255 <when value="BLOSUM45"> | |
| 256 <param name="gap_costs" type="select" label="Gap Costs"> | |
| 257 <option value="">Use Defaults</option> | |
| 258 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option> | |
| 259 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option> | |
| 260 <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option> | |
| 261 <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option> | |
| 262 <option value="-gapopen 15 -gapextend 2" selected="true">Existense: 15 Extension: 2 (default)</option> | |
| 263 <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option> | |
| 264 <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option> | |
| 265 <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option> | |
| 266 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option> | |
| 267 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option> | |
| 268 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option> | |
| 269 <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option> | |
| 270 </param> | |
| 271 </when> | |
| 272 <when value="PAM250"> | |
| 273 <param name="gap_costs" type="select" label="Gap Costs"> | |
| 274 <option value="">Use Defaults</option> | |
| 275 <option value="-gapopen 15 -gapextend 3">Existense: 15 Extension: 3</option> | |
| 276 <option value="-gapopen 14 -gapextend 3">Existense: 14 Extension: 3</option> | |
| 277 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option> | |
| 278 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option> | |
| 279 <option value="-gapopen 17 -gapextend 2">Existense: 17 Extension: 2</option> | |
| 280 <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option> | |
| 281 <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option> | |
| 282 <option value="-gapopen 14 -gapextend 2" selected="true">Existense: 14 Extension: 2 (default)</option> | |
| 283 <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option> | |
| 284 <option value="-gapopen 21 -gapextend 1">Existense: 21 Extension: 1</option> | |
| 285 <option value="-gapopen 20 -gapextend 1">Existense: 20 Extension: 1</option> | |
| 286 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option> | |
| 287 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option> | |
| 288 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option> | |
| 289 </param> | |
| 290 | |
| 291 </when> | |
| 292 <when value="PAM70"> | |
| 293 <param name="gap_costs" type="select" label="Gap Costs"> | |
| 294 <option value="">Use Defaults</option> | |
| 295 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> | |
| 296 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> | |
| 297 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> | |
| 298 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option> | |
| 299 <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option> | |
| 300 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> | |
| 301 </param> | |
| 302 | |
| 303 </when> | |
| 304 <when value="PAM30"> | |
| 305 <param name="gap_costs" type="select" label="Gap Costs"> | |
| 306 <option value="">Use Defaults</option> | |
| 307 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> | |
| 308 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> | |
| 309 <option value="-gapopen 5 -gapextend 2">Existense: 5 Extension: 2</option> | |
| 310 <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option> | |
| 311 <option value="-gapopen 9 -gapextend 1" selected="true">Existense: 9 Extension: 1 (default)</option> | |
| 312 <option value="-gapopen 8 -gapextend 1">Existense: 8 Extension: 1</option> | |
| 313 </param> | |
| 314 </when> | |
| 315 <!-- | |
| 316 Can't use '-ungapped' on its own, error back is: | |
| 317 Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search | |
| 318 Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' | |
| 319 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> | |
| 320 --> | |
| 321 </conditional> | |
| 322 | |
| 323 <!-- I'd like word_size to be optional, with minimum 2 for blastp --> | |
| 324 <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2"> | |
| 325 <validator type="in_range" min="2" /> | |
| 326 </param> | |
| 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"> | |
| 328 <validator type="in_range" min="0" /> | |
| 329 </param> | |
| 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"> | |
| 331 <validator type="in_range" min="1" /> | |
| 332 </param> | |
| 333 <param name="comp_based_stats" type="select" optional="true" label="Use composition-based statistics" | |
| 334 help="Recommended: blastp: 2 blastp-short: 0"> | |
| 335 <option value="">Leave Unspecified</option> | |
| 336 <option value="0">0 or F (No composition-based statistics)</option> | |
| 337 <option value="1">1 (Composition-based statistics as in NAR 29:2994-3005, 2001)</option> | |
| 338 <option value="2">2, T, or D (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties)</option> | |
| 339 <option value="3">3 (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally)</option> | |
| 340 </param> | |
| 341 | |
| 342 <param name="use_sw_tback" type="boolean" label="Compute locally optimal Smith-Waterman alignments?" truevalue="-use_sw_tback" falsevalue="" checked="false" /> | |
| 343 | |
| 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"/> | |
| 345 </when> | |
| 346 </conditional> | |
| 347 </inputs> | |
| 348 | |
| 349 <outputs> | |
| 350 <data name="output_tabular" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> | |
| 351 <filter>fmt_opt['out_format'] == "tabular"</filter> | |
| 352 </data> | |
| 353 <data name="output_xml" format="blastxml" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> | |
| 354 <filter>fmt_opt['out_format'] == "blastxml"</filter> | |
| 355 </data> | |
| 356 <data name="output_txt" format="txt" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> | |
| 357 <filter>fmt_opt['out_format'] == "text" and not fmt_opt['html']</filter> | |
| 358 </data> | |
| 359 <data name="output_html" format="html" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> | |
| 360 <filter>fmt_opt['out_format'] == "text" and fmt_opt['html']</filter> | |
| 361 </data> | |
| 362 </outputs> | |
| 363 | |
| 364 <stdio> | |
| 365 <exit_code range="1" level="fatal" description="Bad input dataset or BLAST options" /> | |
| 366 <exit_code range="2" level="fatal" description="Error in BLAST database" /> | |
| 367 <exit_code range="3" level="fatal" description="Error in BLAST engine" /> | |
| 368 <exit_code range="4" level="fatal" description="Out of Memory" /> | |
| 369 <exit_code range="5:" level="fatal" description="Unknown Error" /> | |
| 370 </stdio> | |
| 371 | |
| 372 <tests> | |
| 373 <test> | |
| 374 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> | |
| 375 <param name="db_opts_selector" value="file" /> | |
| 376 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> | |
| 377 <param name="database" value="" /> | |
| 378 <param name="evalue_cutoff" value="1e-8" /> | |
| 379 <param name="blast_type" value="blastp" /> | |
| 380 <param name="out_format" value="blastxml" /> | |
| 381 <param name="outfmt" value="5" /> | |
| 382 <param name="adv_opts_selector" value="advanced" /> | |
| 383 <param name="filter_query" value="False" /> | |
| 384 <param name="matrix" value="BLOSUM62" /> | |
| 385 <param name="max_target_seqs" value="" /> | |
| 386 <param name="word_size" value="" /> | |
| 387 <param name="parse_deflines" value="True" /> | |
| 388 <output name="output_xml"> | |
| 389 <assert_contents> | |
| 390 <has_text text="sp|Q9BS26|ERP44_HUMAN"/> | |
| 391 </assert_contents> | |
| 392 </output> | |
| 393 </test> | |
| 394 <test> | |
| 395 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> | |
| 396 <param name="db_opts_selector" value="file" /> | |
| 397 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> | |
| 398 <param name="database" value="" /> | |
| 399 <param name="evalue_cutoff" value="1e-8" /> | |
| 400 <param name="blast_type" value="blastp" /> | |
| 401 <param name="out_format" value="tabular" /> | |
| 402 <param name="outfmt" value="6" /> | |
| 403 <param name="adv_opts_selector" value="advanced" /> | |
| 404 <param name="filter_query" value="False" /> | |
| 405 <param name="matrix" value="BLOSUM62" /> | |
| 406 <param name="max_target_seqs" value="" /> | |
| 407 <param name="word_size" value="" /> | |
| 408 <param name="parse_deflines" value="True" /> | |
| 409 <output name="output_tabular"> | |
| 410 <assert_contents> | |
| 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+" /> | |
| 412 <has_text text="BAB21486.1"/> | |
| 413 </assert_contents> | |
| 414 </output> | |
| 415 </test> | |
| 416 <test> | |
| 417 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> | |
| 418 <param name="db_opts_selector" value="file" /> | |
| 419 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> | |
| 420 <param name="database" value="" /> | |
| 421 <param name="evalue_cutoff" value="1e-8" /> | |
| 422 <param name="blast_type" value="blastp" /> | |
| 423 <param name="out_format" value="tabular" /> | |
| 424 <param name="outfmt" value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" /> | |
| 425 <param name="adv_opts_selector" value="advanced" /> | |
| 426 <param name="filter_query" value="False" /> | |
| 427 <param name="matrix" value="BLOSUM62" /> | |
| 428 <param name="max_target_seqs" value="" /> | |
| 429 <param name="word_size" value="" /> | |
| 430 <param name="parse_deflines" value="True" /> | |
| 431 <output name="output_tabular"> | |
| 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+" /> | |
| 434 </assert_contents> | |
| 435 </output> | |
| 436 </test> | |
| 437 <test> | |
| 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+" /> | |
| 450 <has_text text="BAB21486.1"/> | |
| 451 </assert_contents> | |
| 452 </output> | |
| 453 </test> | |
| 454 </tests> | |
| 455 <help> | |
| 456 | |
| 457 .. class:: warningmark | |
| 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> |