comparison tools/ncbi_blast_plus/ncbi_blastp_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_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.00">
    <description>Search protein 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" merge_outputs="output1" />
    <macros>
        <token name="@BINARY@">blastp</token>

#if $adv_opts.adv_opts_selector=="advanced":
-matrix $adv_opts.matrix
@ADVANCED_OPTIONS@
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
## End of advanced options:
#end if
    </command>

    <expand macro="stdio" />

            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 blastp 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>
    </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_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.01">
    <description>Search protein 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" merge_outputs="output1" />
    <macros>
        <token name="@BINARY@">blastp</token>

#if $adv_opts.adv_opts_selector=="advanced":
-matrix $adv_opts.matrix
@ADVANCED_OPTIONS@
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
@ADV_ID_LIST_FILTER@
## End of advanced options:
#end if
    </command>

    <expand macro="stdio" />

            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 blastp 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>
    </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>