<tool id="cap3" name="cap3" version="1.0.1">
<description>Sequence Assembly tool</description>
    <requirements>
    	<requirement type="package" version="3">cap3</requirement>
    </requirements>
<command>
cap3 "$inputSequences" > "$cap3stdout";
                mv "$inputSequences".cap.contigs $contigs;
                mv "$inputSequences".cap.contigs.qual $contigsqual;
                mv "$inputSequences".cap.contigs.links $contigslink;
                mv "$inputSequences".cap.ace $ace;
                mv "$inputSequences".cap.info $info;
                mv "$inputSequences".cap.singlets $singlets;

</command>

        <inputs>
        	<param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" />
        </inputs>

<outputs>
        	<data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output"/>
                <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" />
                <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="True" />
                <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="True" />
                <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="True" />
                <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="True" />
                <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" hidden="True" />
</outputs>

<help>

</help>
</tool>