<tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.0">
    <description></description>
    <macros>
        <import>vsearch_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
    vsearch
        @GENERAL@
        --abskew $abskew
        --chimeras $outfile
        --dn $dn
        --mindiffs $mindiffs
        --mindiv $mindiv
        --minh $minh
        --xn $xn
        $self_param
        $selfid_param
        #if $detection_mode.detection_mode_select == 'denovo':
            --uchime_denovo $detection_mode.infile_denovo
        #else:
            --uchime_ref $detection_mode.infile_reference
            --db $detection_mode.db
        #end if

        #if 'nonchimeras' in str($outputs):
            --nonchimeras $nonchimeras
        #end if
        #if 'uchimealns' in str($outputs):
            --uchimealns $uchimealns
        #end if
        #if 'uchimeout' in str($outputs):
            --uchimeout $uchimeout
        #end if

]]>
    </command>
    <inputs>
        <conditional name="detection_mode">
            <param name="detection_mode_select" type="select" label="Detect chimeras" help="">
                <option value="denovo">de novo</option>
                <option value="reference">using a reference database</option>
            </param>
            <when value="denovo">
                <param name="infile_denovo" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_denovo)" />
            </when>
            <when value="reference">
                <param name="infile_reference" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_ref)" />
                <param name="db" type="data" format="fasta" label="Select your reference database" help="(--db)" />
          </when>
        </conditional>

        <param name="abskew" type="float" value="2.0" label="Minimal abundance ratio of parent vs chimera"
            help="(--abskew)"/>
        <param name="dn" type="float" value="1.4" label="'no' vote pseudo count"
            help="(--dn)"/>
        <param name="xn" type="float" value="8.0" label="'no' vote weight"
            help="(--xn)"/>
        <param name="mindiffs" type="integer" value="3" label="Minimum number of differences in segment"
            help="(--mindiffs)"/>
        <param name="mindiv" type="float" value="0.8" label="Minimum divergence from closest parent"
            help="(--mindiv)"/>
        <param name="minh" type="float" value="0.28" label="Minimum score"
            help="(--minh)"/>

        <expand macro="self_and_selfid" />

        <param name="outputs" type="select" multiple="True" optional="True"
            label="Select output formats" help="(--qmask)">
            <option value="nonchimeras">Non-chimeric sequences (--nonchimeras)</option>
            <option value="uchimealns">Chimera alignments (--uchimealns)</option>
            <option value="uchimeout">Chimera info to tab-separated (--uchimeout)</option>
        </param>

    </inputs>
    <outputs>
        <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
        <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera">
            <filter>'nonchimeras' in outputs</filter>
        </data>
        <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments">
            <filter>'uchimealns' in outputs</filter>
        </data>
        <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information">
            <filter>'uchimeout' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="detection_mode_select" value="denovo"/>
            <param name="infile_denovo" value="PR2-18S-rRNA-V4.derep.fsa.bz2" ftype="fasta" />
            <param name="outputs" value="uchimeout"/>
            <output name="outfile" file="chimera_result1.fasta" ftype="fasta" />
            <output name="uchimeout" file="chimera_uchimeout_result1.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Sequence chimera detection based on a different scoring functions.

Chimera detection options
  --abskew REAL               min abundance ratio of parent vs chimera (2.0)
  --alignwidth INT            width of alignment in uchimealn output (80)
  --chimeras FILENAME         output chimeric sequences to file
  --db FILENAME               reference database for --uchime_ref
  --dn REAL                   'no' vote pseudo-count (1.4)
  --mindiffs INT              minimum number of differences in segment (3)
  --mindiv REAL               minimum divergence from closest parent (0.8)
  --minh REAL                 minimum score (0.28)
  --nonchimeras FILENAME      output non-chimeric sequences to file
  --self                      exclude identical labels for --uchime_ref
  --selfid                    exclude identical sequences for --uchime_ref
  --uchime_denovo FILENAME    detect chimeras de novo
  --uchime_ref FILENAME       detect chimeras using a reference database
  --uchimealns FILENAME       output chimera alignments to file
  --uchimeout FILENAME        output to chimera info to tab-separated file
  --uchimeout5                make output compatible with uchime version 5
  --xn REAL                   'no' vote weight (8.0)

@EXTERNAL_DOCUMENTATION@

-------

@REFERENCES@


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