<tool id="samtools_faidx" name="Faidx (SAMtools)" version="1.0.0">
    <description>Index FASTA file using samtools faidx command</description>
    <requirements>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <command>
        ln -s -f $input faidx_in.${input.ext} &amp;&amp;

        samtools faidx

        faidx_in.${input.ext} &amp;&amp;
        cp faidx_in.${input.ext}.fai $output
    </command>
    <inputs>
        <param name="input" type="data" label="FASTA input file" />
    </inputs>
    <outputs>
        <data name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <help>
**About this tool**

**Samtools faidx**: Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. Outputs index of input file.

More info here: http://www.htslib.org/doc/samtools.html
  </help>
</tool>