comparison tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 14:2fe07f50a41e draft

Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.

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>

@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
## End of advanced options:
#end if
    </command>

    <expand macro="stdio" />

            <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4.">
                <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>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@">
            <expand macro="output_change_format" />

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

@REFERENCES@
    </help>
</tool>

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>

@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" />

            <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4.">
                <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" />

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

@REFERENCES@
    </help>
    <expand macro="blast_citations" />
</tool>