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<tool id="trimal" name="trimAl: a tool for automated alignment trimming" version="0.1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="1.4.1">trimal</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[    
        trimal -in $input1 -out $trimmed_output -htmlout $html_summary ${out_format_selector}
        #if $trimming_mode.mode_selector == "custom"
            -gapthreshold $trimming_mode.gapthreshold
            -simthreshold $trimming_mode.simthreshold
            -cons $trimming_mode.cons
        #else:
            $trimming_mode.mode_selector
        #end if
        ;

    ]]></command>
    <inputs>
        <param name="input1" type="data" format="fasta,clustal,pir,phylip,nexus" multiple="false" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" optional="false" />
        <conditional name="trimming_mode">
            <param name="mode_selector" type="select" label="Select trimming mode from the list">
                <option value="-nogaps">nogaps. Remove all positions with gaps in the alignment.</option>
                <option value="-noallgaps">noallgaps. Remove columns composed only by gaps.</option>
                <option value="-gappyout">gappyout. Only uses information based on gaps' distribution. (see User Guide)</option>
                <option value="-strict">strict. (see User Guide)</option>
                <option value="-strictplus">strictplus. (see User Guide)</option>
                <option value="custom">Custom mode</option>
            </param>
            <when value="custom">
                <param argument="-gapthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="gap threshold" help="1 - (fraction of sequences with a gap allowed). Range: [0 - 1]" multiple="false"/>
                <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="similarity threshold" help="Minimum average similarity allowed. Range: [0 - 1]" multiple="false"/>
                <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="min conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve." multiple="false"/>
                
            </when>
        </conditional>
        <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list">
            <option value="-clustal">CLUSTAL format</option>
            <option value="-fasta">FASTA format</option>
            <option value="-fasta_m10">FASTA format. Sequences name length up to 10 characters.</option>
            <option value="-nbrf">NBRF/PIR format</option>
            <option value="-nexus">NEXUS format</option>
            <option value="-mega">MEGA format</option>
            <option value="-phylip">PHYLIP/PHYLIP4 format</option>
            <option value="-phylip_m10">PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters</option>
            <option value="-phylip_paml">PHYLIP format compatible with PAML</option>
            <option value="-phylip_paml_m10">PHYLIP format compatible with PAML. Sequences name length up to 10 characters.</option>
            <option value="-phylip3.2">PHYLIP3.2 format</option>
            <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option>
        </param>
    </inputs>
    <outputs>
        <data name="trimmed_output" format="fasta" label="Trimmed alignment."/>
        <data name="html_summary" format="html" label="trimal html summary."/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="example.009.AA.fasta"/>
            <param name="mode_selector" value="-gappyout" />
            <param name="out_format_selector" value="-mega" />
            <output name="trimmed_output" file="trimmed_example.009.AA.mega" lines_diff="2"/>
            <output name="html_summary" file="trimmed_example.009.AA.html"/>
        </test>
        <test>
            <param name="input1" value="example.009.AA.fasta"/>
            <param name="mode_selector" value="custom" />
            <param name="gapthreshold" value="0.5" />
            <param name="simthreshold" value="0.5" />
            <param name="cons" value="5" />
            <param name="out_format_selector" value="-phylip_paml_m10" />
            <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" />
            <output name="html_summary" file="custom_trimmed_example.009.AA.html"/>
        </test>
    </tests>
    <help><![CDATA[
Modes
    -nogaps                  Remove all positions with gaps in the alignment.
    -noallgaps               Remove columns composed only by gaps.
    -gappyout                Use automatic selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide).
    -strict                  Use automatic selection on "strict" mode. (see User Guide).
    -strictplus              Use automatic selection on "strictplus" mode. (see User Guide).
    trimAl v1.4.rev15 build[2013-12-17]. 2009-2013. Salvador Capella-Gutierrez and Toni Gabaldón.

Custom mode parameters
    -gt -gapthreshold <n>    1 - (fraction of sequences with a gap allowed).
    -st -simthreshold <n>    Minimum average similarity allowed.
    -cons <n>                Minimum percentage of the positions in the original alignment to conserve.

Output formats
    -nbrf                    Output file in NBRF/PIR format
    -mega                    Output file in MEGA format
    -nexus                   Output file in NEXUS format
    -clustal                 Output file in CLUSTAL format
    -fasta                   Output file in FASTA format
    -fasta_m10               Output file in FASTA format. Sequences name length up to 10 characters.
    -phylip                  Output file in PHYLIP/PHYLIP4 format
    -phylip_m10              Output file in PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters.
    -phylip_paml             Output file in PHYLIP format compatible with PAML
    -phylip_paml_m10         Output file in PHYLIP format compatible with PAML. Sequences name length up to 10 characters.
    -phylip3.2               Output file in PHYLIP3.2 format
    -phylip3.2_m10           Output file in PHYLIP3.2 format. Sequences name length up to 10 characters.
    
trimAl webpage: http://trimal.cgenomics.org

This program is free software: you can redistribute it and/or modify 
it under the terms of the GNU General Public License as published by 
the Free Software Foundation, the last available version.

Please cite:
    trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
    Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon.
    Bioinformatics 2009, 25:1972-1973.
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubTrimAl,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {TrimAl},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/inab/trimal},
}</citation>
    </citations>
</tool>