/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
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1<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11"> 2 <description>Search translated nucleotide database with protein query sequence(s)</description> 3 <version_command>tblastn -version</version_command> 4 <command interpreter="python">hide_stderr.py 5## The command is a Cheetah template which allows some Python based syntax. 6## Lines starting hash hash are comments. Galaxy will turn newlines into spaces 7tblastn 8-query "$query" 9#if $db_opts.db_opts_selector == "db": 10 -db "${db_opts.database.fields.path}" 11#else: 12 -subject "$db_opts.subject" 13#end if 14-evalue $evalue_cutoff 15-out $output1 16##Set the extended list here so if/when we add things, saved workflows are not affected 17#if str($out_format)=="ext": 18 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" 19#else: 20 -outfmt $out_format 21#end if 22-num_threads 8 23#if $adv_opts.adv_opts_selector=="advanced": 24$adv_opts.filter_query 25-matrix $adv_opts.matrix 26## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string 27## Note -max_target_seqs overrides -num_descriptions and -num_alignments 28#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): 29-max_target_seqs $adv_opts.max_hits 30#end if 31#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): 32-word_size $adv_opts.word_size 33#end if 34##Ungapped disabled for now - see comments below 35##$adv_opts.ungapped 36$adv_opts.parse_deflines 37## End of advanced options: 38#end if 39 </command> 40 <inputs> 41 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 42 <conditional name="db_opts"> 43 <param name="db_opts_selector" type="select" label="Subject database/sequences"> 44 <option value="db" selected="True">BLAST Database</option> 45 <option value="file">FASTA file</option> 46 </param> 47 <when value="db"> 48 <param name="database" type="select" label="Nucleotide BLAST database"> 49 <options from_file="blastdb.loc"> 50 <column name="value" index="0"/> 51 <column name="name" index="1"/> 52 <column name="path" index="2"/> 53 </options> 54 </param> 55 <param name="subject" type="hidden" value="" /> 56 </when> 57 <when value="file"> 58 <param name="database" type="hidden" value="" /> 59 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> 60 </when> 61 </conditional> 62 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> 63 <param name="out_format" type="select" label="Output format"> 64 <option value="6" selected="True">Tabular (standard 12 columns)</option> 65 <option value="ext">Tabular (extended 24 columns)</option> 66 <option value="5">BLAST XML</option> 67 <option value="0">Pairwise text</option> 68 <option value="0 -html">Pairwise HTML</option> 69 <option value="2">Query-anchored text</option> 70 <option value="2 -html">Query-anchored HTML</option> 71 <option value="4">Flat query-anchored text</option> 72 <option value="4 -html">Flat query-anchored HTML</option> 73 <!-- 74 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> 75 --> 76 </param> 77 <conditional name="adv_opts"> 78 <param name="adv_opts_selector" type="select" label="Advanced Options"> 79 <option value="basic" selected="True">Hide Advanced Options</option> 80 <option value="advanced">Show Advanced Options</option> 81 </param> 82 <when value="basic" /> 83 <when value="advanced"> 84 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> 85 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> 86 <param name="matrix" type="select" label="Scoring matrix"> 87 <option value="BLOSUM90">BLOSUM90</option> 88 <option value="BLOSUM80">BLOSUM80</option> 89 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> 90 <option value="BLOSUM50">BLOSUM50</option> 91 <option value="BLOSUM45">BLOSUM45</option> 92 <option value="PAM250">PAM250</option> 93 <option value="PAM70">PAM70</option> 94 <option value="PAM30">PAM30</option> 95 </param> 96 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> 97 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> 98 <validator type="in_range" min="0" /> 99 </param> 100 <!-- I'd like word_size to be optional, with minimum 2 for blastp --> 101 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> 102 <validator type="in_range" min="0" /> 103 </param> 104 <!-- 105 Can't use '-ungapped' on its own, error back is: 106 Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search 107 Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.' 108 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> 109 --> 110 <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"/> 111 </when> 112 </conditional> 113 </inputs> 114 <outputs> 115 <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"> 116 <change_format> 117 <when input="out_format" value="0" format="txt"/> 118 <when input="out_format" value="0 -html" format="html"/> 119 <when input="out_format" value="2" format="txt"/> 120 <when input="out_format" value="2 -html" format="html"/> 121 <when input="out_format" value="4" format="txt"/> 122 <when input="out_format" value="4 -html" format="html"/> 123 <when input="out_format" value="5" format="blastxml"/> 124 </change_format> 125 </data> 126 </outputs> 127 <requirements> 128 <requirement type="binary">tblastn</requirement> 129 </requirements> 130 <tests> 131 <test> 132 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> 133 <param name="db_opts_selector" value="file" /> 134 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> 135 <param name="database" value="" /> 136 <param name="evalue_cutoff" value="1e-10" /> 137 <param name="out_format" value="5" /> 138 <param name="adv_opts_selector" value="advanced" /> 139 <param name="filter_query" value="false" /> 140 <param name="matrix" value="BLOSUM80" /> 141 <param name="max_hits" value="0" /> 142 <param name="word_size" value="0" /> 143 <param name="parse_deflines" value="false" /> 144 <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" /> 145 </test> 146 <test> 147 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> 148 <param name="db_opts_selector" value="file" /> 149 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> 150 <param name="database" value="" /> 151 <param name="evalue_cutoff" value="1e-10" /> 152 <param name="out_format" value="ext" /> 153 <param name="adv_opts_selector" value="advanced" /> 154 <param name="filter_query" value="false" /> 155 <param name="matrix" value="BLOSUM80" /> 156 <param name="max_hits" value="0" /> 157 <param name="word_size" value="0" /> 158 <param name="parse_deflines" value="false" /> 159 <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> 160 </test> 161 <test> 162 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> 163 <param name="db_opts_selector" value="file" /> 164 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> 165 <param name="database" value="" /> 166 <param name="evalue_cutoff" value="1e-10" /> 167 <param name="out_format" value="6" /> 168 <param name="adv_opts_selector" value="advanced" /> 169 <param name="filter_query" value="false" /> 170 <param name="matrix" value="BLOSUM80" /> 171 <param name="max_hits" value="0" /> 172 <param name="word_size" value="0" /> 173 <param name="parse_deflines" value="false" /> 174 <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> 175 </test> 176 <test> 177 <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference --> 178 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> 179 <param name="db_opts_selector" value="file" /> 180 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> 181 <param name="database" value="" /> 182 <param name="evalue_cutoff" value="1e-10" /> 183 <param name="out_format" value="6" /> 184 <param name="adv_opts_selector" value="advanced" /> 185 <param name="filter_query" value="false" /> 186 <param name="matrix" value="BLOSUM80" /> 187 <param name="max_hits" value="0" /> 188 <param name="word_size" value="0" /> 189 <param name="parse_deflines" value="true" /> 190 <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> 191 </test> 192 <test> 193 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> 194 <param name="db_opts_selector" value="file" /> 195 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> 196 <param name="database" value="" /> 197 <param name="evalue_cutoff" value="1e-10" /> 198 <param name="out_format" value="0 -html" /> 199 <param name="adv_opts_selector" value="advanced" /> 200 <param name="filter_query" value="false" /> 201 <param name="matrix" value="BLOSUM80" /> 202 <param name="max_hits" value="0" /> 203 <param name="word_size" value="0" /> 204 <param name="parse_deflines" value="false" /> 205 <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" /> 206 </test> 207 </tests> 208 <help> 209 210.. class:: warningmark 211 212**Note**. Database searches may take a substantial amount of time. 213For large input datasets it is advisable to allow overnight processing. 214 215----- 216 217**What it does** 218 219Search a *translated nucleotide database* using a *protein query*, 220using the NCBI BLAST+ tblastn command line tool. 221 222----- 223 224**Output format** 225 226Because Galaxy focuses on processing tabular data, the default output of this 227tool is tabular. The standard BLAST+ tabular output contains 12 columns: 228 229====== ========= ============================================ 230Column NCBI name Description 231------ --------- -------------------------------------------- 232 1 qseqid Query Seq-id (ID of your sequence) 233 2 sseqid Subject Seq-id (ID of the database hit) 234 3 pident Percentage of identical matches 235 4 length Alignment length 236 5 mismatch Number of mismatches 237 6 gapopen Number of gap openings 238 7 qstart Start of alignment in query 239 8 qend End of alignment in query 240 9 sstart Start of alignment in subject (database hit) 241 10 send End of alignment in subject (database hit) 242 11 evalue Expectation value (E-value) 243 12 bitscore Bit score 244====== ========= ============================================ 245 246The BLAST+ tools can optionally output additional columns of information, 247but this takes longer to calculate. Most (but not all) of these columns are 248included by selecting the extended tabular output. The extra columns are 249included *after* the standard 12 columns. This is so that you can write 250workflow filtering steps that accept either the 12 or 24 column tabular 251BLAST output. 252 253====== ============= =========================================== 254Column NCBI name Description 255------ ------------- ------------------------------------------- 256 13 sallseqid All subject Seq-id(s), separated by a ';' 257 14 score Raw score 258 15 nident Number of identical matches 259 16 positive Number of positive-scoring matches 260 17 gaps Total number of gaps 261 18 ppos Percentage of positive-scoring matches 262 19 qframe Query frame 263 20 sframe Subject frame 264 21 qseq Aligned part of query sequence 265 22 sseq Aligned part of subject sequence 266 23 qlen Query sequence length 267 24 slen Subject sequence length 268====== ============= =========================================== 269 270The third option is BLAST XML output, which is designed to be parsed by 271another program, and is understood by some Galaxy tools. 272 273You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). 274The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. 275The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. 276The two query anchored outputs show a multiple sequence alignment between the query and all the matches, 277and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). 278 279------- 280 281**References** 282 283Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. 284 285 </help> 286</tool>