annotate tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @ 3:643338ac83c0 draft

Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.

<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.12">
    <description>Search translated nucleotide database with protein query sequence(s)</description>
    <!-- If job splitting is enabled, break up the query file into parts -->
    <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism>
    <version_command>tblastn -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
tblastn
-query "$query"
#if $db_opts.db_opts_selector == "db":
  -db "${db_opts.database.fields.path}"
#else:
  -subject "$db_opts.subject"
#end if
-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":
-db_gencode $adv_opts.db_gencode
$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 (pairwise e-values)</option>
            </param>
            <when value="db">
                <param name="database" type="select" label="Nucleotide BLAST database">
                    <options from_file="blastdb.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="Nucleotide FASTA file to use as database"/> 
            </when>
        </conditional>
        <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">
                <param name="db_gencode" type="select" label="Database/subject genetic code">
                    <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
                    <option value="1" select="True">1. Standard</option>
                    <option value="2">2. Vertebrate Mitochondrial</option>
                    <option value="3">3. Yeast Mitochondrial</option>
                    <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
                    <option value="5">5. Invertebrate Mitochondrial</option>
                    <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
                    <option value="9">9. Echinoderm Mitochondrial</option>
                    <option value="10">10. Euplotid Nuclear</option>
                    <option value="11">11. Bacteria and Archaea</option>
                    <option value="12">12. Alternative Yeast Nuclear</option>
                    <option value="13">13. Ascidian Mitochondrial</option>
                    <option value="14">14. Flatworm Mitochondrial</option>
                    <option value="15">15. Blepharisma Macronuclear</option>
                    <option value="16">16. Chlorophycean Mitochondrial Code</option>
                    <option value="21">21. Trematode Mitochondrial Code</option>
                    <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
                    <option value="23">23. Thraustochytrium Mitochondrial Code</option>
                    <option value="24">24. Pterobranchia mitochondrial code</option>
                </param>
                <!-- 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="true" />
                <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 tblastn 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="tblastn 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">tblastn</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_nucs.fasta" ftype="fasta" />
            <param name="database" value="" />
            <param name="evalue_cutoff" value="1e-10" />
            <param name="out_format" value="5" />
            <param name="adv_opts_selector" value="advanced" />
            <param name="filter_query" value="false" />
            <param name="matrix" value="BLOSUM80" />
            <param name="max_hits" value="0" />
            <param name="word_size" value="0" />
            <param name="parse_deflines" value="false" />
            <output name="output1" file="tblastn_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_nucs.fasta" ftype="fasta" />
            <param name="database" value="" />
            <param name="evalue_cutoff" value="1e-10" />
            <param name="out_format" value="ext" />
            <param name="adv_opts_selector" value="advanced" />
            <param name="filter_query" value="false" />
            <param name="matrix" value="BLOSUM80" />
            <param name="max_hits" value="0" />
            <param name="word_size" value="0" />
            <param name="parse_deflines" value="false" />
            <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.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_nucs.fasta" ftype="fasta" />
            <param name="database" value="" />
            <param name="evalue_cutoff" value="1e-10" />
            <param name="out_format" value="6" />
            <param name="adv_opts_selector" value="advanced" />
            <param name="filter_query" value="false" />
            <param name="matrix" value="BLOSUM80" />
            <param name="max_hits" value="0" />
            <param name="word_size" value="0" />
            <param name="parse_deflines" value="false" />
            <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
        </test>
        <test>
            <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference -->
            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
            <param name="db_opts_selector" value="file" />
            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
            <param name="database" value="" />
            <param name="evalue_cutoff" value="1e-10" />
            <param name="out_format" value="6" />
            <param name="adv_opts_selector" value="advanced" />
            <param name="filter_query" value="false" />
            <param name="matrix" value="BLOSUM80" />
            <param name="max_hits" value="0" />
            <param name="word_size" value="0" />
            <param name="parse_deflines" value="true" />
            <output name="output1" file="tblastn_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_nucs.fasta" ftype="fasta" />
            <param name="database" value="" />
            <param name="evalue_cutoff" value="1e-10" />
            <param name="out_format" value="0 -html" />
            <param name="adv_opts_selector" value="advanced" />
            <param name="filter_query" value="false" />
            <param name="matrix" value="BLOSUM80" />
            <param name="max_hits" value="0" />
            <param name="word_size" value="0" />
            <param name="parse_deflines" value="false" />
            <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" />
        </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 *translated nucleotide database* using a *protein query*,
using the NCBI BLAST+ tblastn 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.

    </help>
</tool>