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