plastx.xml

<tool id="plastx" name="plastx" version="0.0.1">
    <description>Search protein database with translated nucleotide query sequence(s)</description>
    <macros>
        <token name="@BINARY@">plastx</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 plastx
-i "$query"
@PLAST_DB_SUBJECT_PROT@
@BASIC_PARAMS@
-e $evalue_cutoff
-o "$output1"
-outfmt 2
-nohit false
#if $ext_param.ext_param_selector=="extended":
$ext_param.filter_query
-M $ext_param.matrix
$ext_param.gap_costs
#end if
#if $config_param.config_param_selector=="advanced":
-a $config_param.nb_threads
-max-database-size $config_param.max_db_size
-seeds-use-ratio $config_param.percent_seed
-s $config_param.ungap_threshold_prot
-n $config_param.ungap_neighboors
-g $config_param.smallgap_threshold
-b $config_param.smallgap_bandwidth
#end if
    </command>
    <expand macro="stdio" />

    <inputs>
        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
        <expand macro="input_conditional_protein_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_scoring_matrix" />
            <expand macro="input_gap_costs" />
        </expand>
        <expand macro="configuration_parameters">
            <expand macro="input_nb_threads" />
            <expand macro="input_max_db_size" />
            <expand macro="input_percent_seed" />
            <expand macro="input_ungap_threshold_prot" />
            <expand macro="input_ungap_neighboors" />
            <expand macro="input_smallgap_threshold" />
            <expand macro="input_smallgap_bandwidth" />
        </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 *protein database* using a *nucleotide query*,
using the Plast command line tool.

@FASTA_WARNING@

-----

@OUTPUT_FORMAT@

    </help>

</tool>