<tool id="vsearch_alignment" name="VSearch alignment" 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@
        $acceptall
        --id "${id}"
        --iddef "${iddef}"
        --allpairs_global "${infile}"
        --alnout "${outfile}"
        #if str( $query_cov ):
            --query_cov "${query_cov}"
        #end if
        @USERFIELDS@
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--allpairs_global)" />
        <expand macro="id_and_iddef" />
        <param name="acceptall" type="boolean" truevalue="--acceptall" falsevalue="" checked="False" 
            label="Output all pairwise alignments" help="This option overrides all other accept/reject options including identity. (--acceptall)"/>
        <param name="query_cov" type="float" value="" optional="True" label="Reject if fraction of query seq. aligned lower than this value"
            help="(--query_cov)"/>
        <expand macro="userfields" />
    </inputs>
    <outputs>
        <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="Rfam_11_0.repr.fasta.bz2" ftype="fasta" />
            <param name="acceptall" value=""/>
            <param name="id" value="0.97"/>
            <param name="query_cov" value="0.95"/>
            <param name="userfields" value="query,target"/>
            <output name="outfile" file="alignment_result1.fasta" lines_diff="4" ftype="fasta" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Pairwise alignments of all sequences.


Alignment options (most searching options also apply)
  --allpairs_global FILENAME  perform global alignment of all sequence pairs
  --alnout FILENAME           filename for human-readable alignment output
  --acceptall                 output all pairwise alignments

@EXTERNAL_DOCUMENTATION@


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