<tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.1">
    <description></description>
    <macros>
        <import>vsearch_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
    vsearch
        @GENERAL@
        #if str( $qmask ) != 'no':
            --qmask "$qmask"
        #end if
        $hardmask
        --maskfasta "$infile"
        --output "$outfile"

]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--maskfasta)" />
        <expand macro="qmask" />
        <expand macro="hardmask" />
    </inputs>
    <outputs>
        <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="db.fasta" ftype="fasta" />
            <param name="qmask" value="dust"/>
            <param name="hardmask" value="True"/>
            <output name="outfile" file="masking_result1.fasta" ftype="fasta" />
        </test>
        <test>
            <param name="infile" value="db.fasta" ftype="fasta" />
            <param name="qmask" value="soft"/>
            <param name="hardmask" value="True"/>
            <output name="outfile" file="masking_result2.fasta" ftype="fasta" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

An input sequence can be composed of lower- or uppercase nucleotides. Lowercase nucleotides
are silently set to uppercase before masking, unless the −−qmask soft option is used.
Here are the results of combined masking options −−qmask (or −−dbmask for database sequences) and −−hardmask, assuming each input sequences contains both lower and uppercase nucleotides:

===== ======== ================================================
qmask hardmask action
===== ======== ================================================
none  off      no masking, all symbols uppercased
none  on       no masking, all symbols uppercased
dust  off      masked symbols lowercased, others uppercased
dust  on       masked symbols changed to Ns, others uppercased
soft  off      lowercase symbols masked, no case changes
soft  on       lowercase symbols masked and changed to Ns
===== ======== ================================================

Masking options
  --hardmask                  mask by replacing with N instead of lower case
  --maskfasta FILENAME        mask sequences in the given FASTA file
  --output FILENAME           output to specified FASTA file
  --qmask                     mask seqs with "dust", "soft" or "none" method (dust)

@EXTERNAL_DOCUMENTATION@


]]>
    </help>
    <expand macro="citations" />
</tool>