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galaxy/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
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<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11">
<description>Search protein database with protein query sequence(s)</description>
<version_command>blastp -version</version_command>
<command interpreter="python">hide_stderr.py
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
blastp
-query "$query"
#if $db_opts.db_opts_selector == "db":
-db "${db_opts.database.fields.path}"
#else:
-subject "$db_opts.subject"
#end if
-task $blast_type
-evalue $evalue_cutoff
-out $output1
##Set the extended list here so if/when we add things, saved workflows are not affected
#if str($out_format)=="ext":
-outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
#else:
-outfmt $out_format
#end if
-num_threads 8
#if $adv_opts.adv_opts_selector=="advanced":
$adv_opts.filter_query
-matrix $adv_opts.matrix
## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
## Note -max_target_seqs overrides -num_descriptions and -num_alignments
#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
-max_target_seqs $adv_opts.max_hits
#end if
#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
-word_size $adv_opts.word_size
#end if
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
$adv_opts.parse_deflines
## End of advanced options:
#end if
</command>
<inputs>
<param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>
<conditional name="db_opts">
<param name="db_opts_selector" type="select" label="Subject database/sequences">
<option value="db" selected="True">BLAST Database</option>
<option value="file">FASTA file</option>
</param>
<when value="db">
<param name="database" type="select" label="Protein BLAST database">
<options from_file="blastdb_p.loc">
<column name="value" index="0"/>
<column name="name" index="1"/>
<column name="path" index="2"/>
</options>
</param>
<param name="subject" type="hidden" value="" />
</when>
<when value="file">
<param name="database" type="hidden" value="" />
<param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/>
</when>
</conditional>
<param name="blast_type" type="select" display="radio" label="Type of BLAST">
<option value="blastp">blastp</option>
<option value="blastp-short">blastp-short</option>
</param>
<param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
<param name="out_format" type="select" label="Output format">
<option value="6" selected="True">Tabular (standard 12 columns)</option>
<option value="ext">Tabular (extended 24 columns)</option>
<option value="5">BLAST XML</option>
<option value="0">Pairwise text</option>
<option value="0 -html">Pairwise HTML</option>
<option value="2">Query-anchored text</option>
<option value="2 -html">Query-anchored HTML</option>
<option value="4">Flat query-anchored text</option>
<option value="4 -html">Flat query-anchored HTML</option>
<!--
<option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-->
</param>
<conditional name="adv_opts">
<param name="adv_opts_selector" type="select" label="Advanced Options">
<option value="basic" selected="True">Hide Advanced Options</option>
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic" />
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
<param name="matrix" type="select" label="Scoring matrix">
<option value="BLOSUM90">BLOSUM90</option>
<option value="BLOSUM80">BLOSUM80</option>
<option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
<option value="BLOSUM50">BLOSUM50</option>
<option value="BLOSUM45">BLOSUM45</option>
<option value="PAM250">PAM250</option>
<option value="PAM70">PAM70</option>
<option value="PAM30">PAM30</option>
</param>
<!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
<param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
<validator type="in_range" min="0" />
</param>
<!-- I'd like word_size to be optional, with minimum 2 for blastp -->
<param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
<validator type="in_range" min="0" />
</param>
<!--
Can't use '-ungapped' on its own, error back is:
Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.'
<param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
-->
<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"/>
</when>
</conditional>
</inputs>
<outputs>
<data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
<change_format>
<when input="out_format" value="0" format="txt"/>
<when input="out_format" value="0 -html" format="html"/>
<when input="out_format" value="2" format="txt"/>
<when input="out_format" value="2 -html" format="html"/>
<when input="out_format" value="4" format="txt"/>
<when input="out_format" value="4 -html" format="html"/>
<when input="out_format" value="5" format="blastxml"/>
</change_format>
</data>
</outputs>
<requirements>
<requirement type="binary">blastp</requirement>
</requirements>
<tests>
<test>
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-8" />
<param name="blast_type" value="blastp" />
<param name="out_format" value="5" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="False" />
<param name="matrix" value="BLOSUM62" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="True" />
<output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
</test>
<test>
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-8" />
<param name="blast_type" value="blastp" />
<param name="out_format" value="6" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="False" />
<param name="matrix" value="BLOSUM62" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="True" />
<output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
</test>
<test>
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-8" />
<param name="blast_type" value="blastp" />
<param name="out_format" value="ext" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="False" />
<param name="matrix" value="BLOSUM62" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="True" />
<output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
</test>
<test>
<param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-8" />
<param name="blast_type" value="blastp" />
<param name="out_format" value="6" />
<param name="adv_opts_selector" value="basic" />
<output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" />
</test>
</tests>
<help>
.. class:: warningmark
**Note**. Database searches may take a substantial amount of time.
For large input datasets it is advisable to allow overnight processing.
-----
**What it does**
Search a *protein database* using a *protein query*,
using the NCBI BLAST+ blastp command line tool.
-----
**Output format**
Because Galaxy focuses on processing tabular data, the default output of this
tool is tabular. The standard BLAST+ tabular output contains 12 columns:
====== ========= ============================================
Column NCBI name Description
------ --------- --------------------------------------------
1 qseqid Query Seq-id (ID of your sequence)
2 sseqid Subject Seq-id (ID of the database hit)
3 pident Percentage of identical matches
4 length Alignment length
5 mismatch Number of mismatches
6 gapopen Number of gap openings
7 qstart Start of alignment in query
8 qend End of alignment in query
9 sstart Start of alignment in subject (database hit)
10 send End of alignment in subject (database hit)
11 evalue Expectation value (E-value)
12 bitscore Bit score
====== ========= ============================================
The BLAST+ tools can optionally output additional columns of information,
but this takes longer to calculate. Most (but not all) of these columns are
included by selecting the extended tabular output. The extra columns are
included *after* the standard 12 columns. This is so that you can write
workflow filtering steps that accept either the 12 or 24 column tabular
BLAST output.
====== ============= ===========================================
Column NCBI name Description
------ ------------- -------------------------------------------
13 sallseqid All subject Seq-id(s), separated by a ';'
14 score Raw score
15 nident Number of identical matches
16 positive Number of positive-scoring matches
17 gaps Total number of gaps
18 ppos Percentage of positive-scoring matches
19 qframe Query frame
20 sframe Subject frame
21 qseq Aligned part of query sequence
22 sseq Aligned part of subject sequence
23 qlen Query sequence length
24 slen Subject sequence length
====== ============= ===========================================
The third option is BLAST XML output, which is designed to be parsed by
another program, and is understood by some Galaxy tools.
You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-------
**References**
Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
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.
</help>
</tool>
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