plastn.xml

<tool id="plastn" name="plastn" version="0.0.1">
    <description>Search nucleotide database with nucleotide query sequence(s)</description>
    <macros>
        <token name="@BINARY@">plastn</token>
        <import>plast_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
Plast
-p plastn
-i "$query"
@PLAST_DB_SUBJECT_NUCL@
@BASIC_PARAMS@
-e $evalue_cutoff
-o "$output1"
-outfmt 2
-nohit false
#if $ext_param.ext_param_selector=="extended":
$ext_param.filter_query
$ext_param.strand
$ext_param.match_mismatch
#end if
#if $config_param.config_param_selector=="advanced":
-a $config_param.nb_threads
-max-database-size $config_param.max_db_size
#if (str($config_param.ungap_threshold_nucl) and int(str($config_param.ungap_threshold_nucl)) > 0):
-s $config_param.ungap_threshold_nucl
#end if
##-xdrop-ungap $config_param.ungap_Xdrop
-X $config_param.gap_Xdrop
-Z $config_param.final_gap_Xdrop
#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" />
        <expand macro="input_evalue" />
        <expand macro="input_max_hits_query" />
        <expand macro="input_max_hsp_hits" />
        <expand macro="extended_parameters">
            <expand macro="input_filter_query_default_true" />
            <expand macro="input_strand" />
            <expand macro="input_match_mismatch" />
        </expand>
        <expand macro="configuration_parameters">
            <expand macro="input_nb_threads" />
            <expand macro="input_max_db_size" />
            <expand macro="input_ungap_threshold_nucl" />
            <!--expand macro="input_ungap_Xdrop" /-->
            <expand macro="input_gap_Xdrop" />
            <expand macro="input_final_gap_Xdrop" />
        </expand>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="@BINARY@ $query.name vs @ON_DB_SUBJECT@"/>
    </outputs>

    <help>
    
@SEARCH_TIME_WARNING@

**What it does**

Search a *nucleotide database* using a *nucleotide query*,
using the Plast command line tool.

@FASTA_WARNING@

-----

@OUTPUT_FORMAT@

    </help>

</tool>