view vref_fasta.xml @ 11:ed2170329841 draft

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<tool id="vref_fasta" name="Virana References">

<description>Obtains NCBI RefSeq and Ensembl reference genomes. </description>

	<requirements>
        <requirement type="package" version="1.0">virana_python</requirement>


    </requirements>

    <command interpreter="python">vref.py fasta --output_file $output 
        
    #if $refseq
        #set $groups = str($refseq).split(",")
        #for $ref in $groups:
            --reference $ref
        #end for
    #end if
    
    
    $zipped
       
    2&gt;&amp;1
    </command>
    
    <inputs>
        <param name="refseq" type="select" label="Set RefSeq taxonomic groups" multiple="true" display="checkboxes">
            <option value="UniVec">UniVec</option>
            <option value="rRNA">rRNA</option>
            <option value="Homo_sapiens">Homo sapiens</option>
            <option value="Fungi">Fungi</option>
            <option value="Plasmids">Plasmids</option>
            <option value="Protozoa">Protozoa</option>
            <option value="Viruses">Viruses</option>
            <option value="Homo_sapiens_cDNA">Homo sapiens cDNA</option>
            <option value="Fungi_DRAFT">Fungi DRAFT</option>
            <option value="Bacteria">Bacteria</option>
            <option value="Bacteria_DRAFT">Bacteria DRAFT</option>
        </param>
        
        <param name="zipped" type="boolean" label="check for zipped output?" truevalue="--zipped" falsevalue=""/>

    </inputs>
    
    
    <outputs>
        <data format="fasta" name="output" label="references.fasta"/>
    </outputs>
</tool>