comparison tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 13:623f727cdff1 draft

Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.

12:6560192c5098

<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.22">
    <description>Search nucleotide database with nucleotide 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" merge_outputs="output1"></parallelism>
    <macros>
        <token name="@BINARY@">blastn</token>

        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 

        <expand macro="input_conditional_nucleotide_db" />

        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
            <option value="megablast">megablast</option>
            <option value="blastn">blastn</option>
            <option value="blastn-short">blastn-short</option>
            <option value="dc-megablast">dc-megablast</option>
            <!-- Using BLAST 2.2.24+ this gives an error:
            BLAST engine error: Program type 'vecscreen' not supported
            <option value="vecscreen">vecscreen</option>
            -->
        </param>
        <expand macro="input_evalue" />
        <expand macro="input_out_format" />
        <expand macro="advanced_options">
            <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->

            <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
            <expand macro="input_parse_deflines" />
        </expand>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="${blast_type.value_label} $query.name vs @ON_DB_SUBJECT@">
            <expand macro="output_change_format" />
        </data>
    </outputs>
    <tests>
        <test>
            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
            <param name="db_opts_selector" value="file" />
            <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
            <param name="database" value="" />
            <param name="evalue_cutoff" value="1e-40" />
            <param name="out_format" value="6" />
            <param name="adv_opts_selector" value="basic" />
            <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
    
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13:623f727cdff1

<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.00">
    <description>Search nucleotide database with nucleotide 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" merge_outputs="output1"></parallelism>
    <macros>
        <token name="@BINARY@">blastn</token>

        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 

        <expand macro="input_conditional_nucleotide_db" />

        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
            <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option>
            <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option>
            <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option>
            <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option>
            <!-- Using BLAST 2.2.24+ this gives an error:
            BLAST engine error: Program type 'vecscreen' not supported
            <option value="vecscreen">vecscreen</option>
            In any case, vecscreen has gone in BLAST+ 2.2.28
            -->
            <!-- BLAST+ 2.2.28 also offers rmblastn -->
        </param>
        <expand macro="input_evalue" />
        <expand macro="input_out_format" />
        <expand macro="advanced_options">
            <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->

            <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
            <expand macro="input_parse_deflines" />
        </expand>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@">
            <expand macro="output_change_format" />
        </data>
    </outputs>
    <tests>
        <test>
            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
            <param name="db_opts_selector" value="file" />
            <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
            <param name="database" value="" />
            <param name="evalue_cutoff" value="1e-40" />
            <param name="out_format" value="5" />
            <param name="adv_opts_selector" value="basic" />
            <output name="output1" file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" />
        </test>
        <test>
            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
            <param name="db_opts_selector" value="file" />
            <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
            <param name="database" value="" />
            <param name="evalue_cutoff" value="1e-40" />
            <param name="out_format" value="6" />
            <param name="adv_opts_selector" value="basic" />
            <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
            <param name="db_opts_selector" value="file" />
            <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
            <param name="database" value="" />
            <param name="evalue_cutoff" value="1e-40" />
            <param name="out_format" value="cols" />
            <param name="std_cols" value="qseqid,sseqid,pident" />
            <param name="ext_cols" value="qlen,slen" />
            <param name="adv_opts_selector" value="basic" />
            <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
    
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