comparison tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @ 22:6f386c5dc4fb draft

v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates

21:7538e2bfcd41

        <token name="@BINARY@">tblastn</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="parallelism" />
    <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
tblastn
-query "$query"
@BLAST_DB_SUBJECT@
-task $blast_type
-evalue $evalue_cutoff
@BLAST_OUTPUT@
@THREADS@

@ADV_QCOV_HSP_PERC@
## End of advanced options:
#end if
    </command>
    <inputs>
        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 

        <expand macro="input_conditional_nucleotide_db" />
        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
            <option value="tblastn">tblastn - Traditional TBLASTN to compare protein query to translated nucleotide database</option>
            <option value="tblastn-fast">tblastn-fast - Use longer words for seeding, faster but less accurate</option>
        </param>
        <expand macro="input_evalue" />
        <expand macro="input_out_format" />

            <expand macro="input_word_size" />
            <!--
            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" />
            -->
            <expand macro="input_parse_deflines" />
            <expand macro="advanced_optional_id_files" />
            <expand macro="input_qcov_hsp_perc" />
        </expand>

            <param name="parse_deflines" value="false" />
            <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" lines_diff="8" />
        </test>
    </tests>
    <help>
    
@SEARCH_TIME_WARNING@

**What it does**

Search a *translated nucleotide database* using a *protein query*,

22:6f386c5dc4fb

        <token name="@BINARY@">tblastn</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="parallelism" />
    <expand macro="preamble" />
    <command detect_errors="aggressive">
## 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'
@BLAST_DB_SUBJECT@
-task $blast_type
-evalue $evalue_cutoff
@BLAST_OUTPUT@
@THREADS@

@ADV_QCOV_HSP_PERC@
## End of advanced options:
#end if
    </command>
    <inputs>
        <param argument="-query" type="data" format="fasta" label="Protein query sequence(s)"/>

        <expand macro="input_conditional_nucleotide_db" />
        <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST">
            <option value="tblastn">tblastn - Traditional TBLASTN to compare protein query to translated nucleotide database</option>
            <option value="tblastn-fast">tblastn-fast - Use longer words for seeding, faster but less accurate</option>
        </param>
        <expand macro="input_evalue" />
        <expand macro="input_out_format" />

            <expand macro="input_word_size" />
            <!--
            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 argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
            -->
            <expand macro="input_parse_deflines" />
            <expand macro="advanced_optional_id_files" />
            <expand macro="input_qcov_hsp_perc" />
        </expand>

            <param name="parse_deflines" value="false" />
            <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" lines_diff="8" />
        </test>
    </tests>
    <help>

@SEARCH_TIME_WARNING@

**What it does**

Search a *translated nucleotide database* using a *protein query*,