comparison tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 15:c16c30e9ad5b draft

Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)

14:2fe07f50a41e

<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.01">
    <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>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
blastn
-query "$query"

-evalue $evalue_cutoff
@BLAST_OUTPUT@
@THREADS@
#if $adv_opts.adv_opts_selector=="advanced":
$adv_opts.strand
@ADVANCED_OPTIONS@
#if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ):
-perc_identity $adv_opts.identity_cutoff
#end if
$adv_opts.ungapped
@ADV_ID_LIST_FILTER@
## End of advanced options:
#end if
    </command>

    <expand macro="stdio" />

    <inputs>
        <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>

                <validator type="in_range" min="0" />
            </param>
            <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
            <expand macro="input_parse_deflines" />
            <expand macro="advanced_optional_id_files" />
        </expand>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@">
            <expand macro="output_change_format" />

            <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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15:c16c30e9ad5b

<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.03">
    <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>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="preamble" />
    <command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
blastn
-query "$query"

-evalue $evalue_cutoff
@BLAST_OUTPUT@
@THREADS@
#if $adv_opts.adv_opts_selector=="advanced":
$adv_opts.strand
@ADV_FILTER_QUERY@
@ADV_MAX_HITS@
@ADV_WORD_SIZE@
#if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ):
-perc_identity $adv_opts.identity_cutoff
#end if
$adv_opts.ungapped
@ADV_ID_LIST_FILTER@
@ADV_QCOV_HSP_PERC@
## End of advanced options:
#end if
    </command>
    <inputs>
        <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>

                <validator type="in_range" min="0" />
            </param>
            <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
            <expand macro="input_parse_deflines" />
            <expand macro="advanced_optional_id_files" />
            <expand macro="input_qcov_hsp_perc" />
        </expand>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@">
            <expand macro="output_change_format" />

            <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>
        <!-- Disable for ToolShed where *.loc tests not yet supported
             See https://github.com/peterjc/galaxy_blast/issues/53
        <test>
            <param name="query" value="chimera.fasta" ftype="fasta" />
            <param name="db_opts_selector" value="db" />
            <param name="database" value="three_human_mRNA" />
            <param name="out_format" value="6" />
            <param name="adv_opts_selector" value="advanced" />
            <param name="max_hits" value="1" />
            <output name="output1" file="blastn_chimera_vs_three_human_max1.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="query" value="chimera.fasta" ftype="fasta" />
            <param name="db_opts_selector" value="db" />
            <param name="database" value="three_human_mRNA" />
            <param name="out_format" value="0" />
            <param name="adv_opts_selector" value="advanced" />
            <param name="max_hits" value="1" />
            <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" />
        </test>
        -->
    </tests>
    <help>
    
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