<tool id="sfffile" name="Sff File" version="1.0.0">
<description>Select reads to include or exclude from one or more input Sff files</description>
<command>sfffile -$include_or_exclude $list_file -o $output
#for $i in $inputs
${i.input}
#end for
</command>
<inputs>
    <repeat name="inputs" title="Input Files">
        <param name="input" type="data" format="sff" label="Sff file"/>
    </repeat>
    <param name="list_file" type="data" format="text" label="List of read IDs"/>
    <param name="include_or_exclude" type="select" label="Include or exclude the named reads?">
        <option value='i' selected='true'>include</option>
        <option value='e'>exclude</option>
    </param>
</inputs>

<outputs>
    <data name="output" format="sff"/>
</outputs>

<help>

**What it does**

This tool creates an Sff file, either including or excluding named reads.
</help>
</tool>