annotate clipkit.xml @ 2:e9cf321ee7be draft

"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

<tool id="clipkit" name="ClipKIT. Alignment trimming software for phylogenetics." version="0.1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="1.3">clipkit</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[    
        clipkit $input1 -m ${mode_selector} -o $trimmed_output -of $out_format_selector --log ${complement} 
        #if $gaps
            --gaps ${gaps}
        #end if;
        &&
        mv ${trimmed_output}.log ${log_output}
        #if $complement
            &&
            mv ${trimmed_output}.complement ${complement_output}
        #end if;

    ]]></command>
    <inputs>
        <param name="input1" type="data" format="fasta,clustal,maf,xmfa,phylip,stockholm" multiple="false" label="Alignment file" optional="false" />
        <param name="mode_selector" type="select" label="Select trimming mode from the list">
            <option value="smart-gap">smart-gap</option>
            <option value="gappy">gappy</option>
            <option value="kpic">kpic</option>
            <option value="kpic-smart-gap">kpic-smart-gap</option>
            <option value="kpic-gappy">kpic-gappy</option>
            <option value="kpi">kpi</option>
            <option value="kpi-smart-gap">kpi-smart-gap</option>
            <option value="kpi-gappy">kpi-gappy</option>
        </param>
        <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list">
            <option value="fasta">FASTA format</option>
            <option value="clustal">CLUSTAL format</option>
            <option value="maf">MAF format</option>
            <option value="mauve">MAUVE format</option>
            <option value="stockholm">STOCKHOLM format</option>
            <option value="phylip">PHYLIP/PHYLIP4 format</option>
            <option value="phylip_sequential">PHYLIP/PHYLIP4 sequential format</option>
            <option value="phylip_relaxed">PHYLIP/PHYLIP4 relaxed format</option>
        </param>
        <param name="gaps" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="gappyness" help="Specify gappyness threshold (between 0 and 1). Default: 0.9" multiple="false"/>
        <param name="complement" type="boolean" truevalue="--complement" falsevalue="" checked="False" label="create complement of the trimmed alignment" />
    </inputs>
    <outputs>
        <data name="trimmed_output" format="fasta" label="Trimmed alignment."/>
        <data name="log_output" format="txt" label="Clipkit log."/>
        <data name="complement_output" format="fasta" label="Clipkit complement.">
            <filter>complement</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="simple.fa"/>
            <param name="mode_selector" value="smart-gap" />
            <param name="gaps" value="0.9" />
            <output name="trimmed_output" file="simple.fa.clipkit"/>
            <output name="log_output" file="simple.fa.clipkit.log"/>
        </test>
        <test>
            <param name="input1" value="simple.fa"/>
            <param name="mode_selector" value="gappy" />
            <param name="gaps" value="0.2" />
            <output name="trimmed_output" file="gappy.simple.fa.clipkit"/>
        </test>
        <test>
            <param name="input1" value="simple.fa"/>
            <param name="mode_selector" value="gappy" />
            <param name="gaps" value="0.2" />
            <output name="trimmed_output" file="gappy.simple.fa.clipkit"/>
            <output name="log_output" file="gappy.simple.fa.clipkit.log"/>
        </test>
        <test>
            <param name="input1" value="simple.fa"/>
            <param name="mode_selector" value="kpi" />
            <param name="complement" value="true" />
            <param name="gaps" value="0.9" />
            <output name="trimmed_output" file="kpi.simple.fa.clipkit"/>
            <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/>
        </test>
        <test>
            <param name="input1" value="simple.fa"/>
            <param name="mode_selector" value="kpi-gappy" />
            <param name="out_format_selector" value="phylip_relaxed" />
            <param name="gaps" value="0.7" />
            <output name="trimmed_output" file="of.gaps.simple.phylip_relaxed"/>
            <output name="log_output" file="of.gaps.simple.phylip_relaxed.log"/>
        </test>
    </tests>
    <help><![CDATA[         
Modes
    smart-gap: dynamic determination of gaps threshold
    gappy: trim sites that are greater than the gaps threshold
    kpic: keeps parismony informative and constant sites
    kpic-smart-gap: a combination of kpic- and smart-gap-based trimming
    kpic-gappy: a combination of kpic- and gappy-based trimming
    kpi: keep only parsimony informative sites
    kpi-smart-gap: a combination of kpi- and smart-gap-based trimming
    kpi-gappy: a combination of kpi- and gappy-based trimming

Gaps
    Positions with gappyness greater than threshold will be trimmed. 
    Must be between 0 and 1. (Default: 0.9). This argument is ignored
    when using the kpi and kpic mdoes of trimming as well as an 
    iteration of trimming that uses smart-gap.

Input and output file formats
    Supported input and output files include:
    fasta, clustal, maf, mauve, phylip, phylip-sequential, 
    phylip-relaxed, and stockholm

Log
    Creates a log file that summarizes the characteristics of each position.
    The log file has four columns.
    - Column 1 is the position in the alignment (starting at 1), 
    - Column 2 reports if the site was trimmed or kept (trim and keep, respectively),
    - Column 3 reports if the site is a parsimony informative site or not (PI and nPI, respectively), or
    a constant site or not (Const, nConst), or neither (nConst, nPI)
    - Column 4 reports the gappyness of the the position (number of gaps / entries in alignment)

Complementary
    Creates an alignment file of only the trimmed sequences.
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubClipKIT,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {ClipKIT},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/jlsteenwyk/clipkit},
}</citation>
    </citations>
</tool>