<tool id="trimns" name="TrimN" version="0.1.0" profile="20.01">
    <requirements>
        <requirement type="package" version="1.0">trimns_vgp</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        remove_fake_cut_sites_DNAnexus.py '$fasta_in' step1_out.fasta step1.log
        && trim_Ns_DNAnexus.py '$fasta_in' step2_out.list
        && clip_regions_DNAnexus.py step1_out.fasta step2_out.list final_out.fasta
    ]]></command>
    <inputs>
        <param name="fasta_in" type="data" format="fasta" label="Fasta file input" help="Fasta file to trim, and from which to remove Ns and fake cut sites."/>
    </inputs>
    <outputs>
        <data name="trimmed_out" format="fasta" from_work_dir="final_out.fasta" label="${tool.name} on ${on_string}: trimmed fasta file" />
    </outputs>
    <tests>
        <test>
            <param name="fasta_in" value="in.fasta"/>
            <output name="trimmed_out" value="out.fasta" ftype="fasta"/>
        </test>
    </tests> 
    <help><![CDATA[
.. class:: infomark

**What it does**

TrimNs is part of the VGP pipeline, and is made of a series of python scripts which trim off large stretches of N bases and to
remove fake cut sites that sometimes get inserted at the end of bionano hybrid scaffolds.

    ]]></help>
    <citations>
        <citation type="doi">10.1101/2020.05.22.110833</citation>
        <citation type="doi">10.1101/2020.06.30.177956</citation>
    </citations>
</tool>