annotate snipit.xml @ 0:20b4c59bec12 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d

<tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0">
    <description>Summarise snps relative to a reference sequence</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.5</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">snipit</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        snipit '$alignment'
            #if $opt.reference
                -r '$opt.reference'
            #end if
            #if $opt.labels
                -l '$opt.labels'
            #end if
            --l-header '$opt.l_header'
            -f '$opt.format'
            --height '$opt.height'
            --width '$opt.width'
            --size-option '$opt.size_option'
            $opt.flip_vertical
            #if $opt.exclude_positions
                --exclude-positions '$opt.exclude_positions'
            #end if
            $opt.exclude_ambig_pos
            $opt.sort_by_mutation_number
            $opt.sort_by_id
            #if $opt.sort_by_mutations
                --sort-by-mutations '$opt.sort_by_mutations'
            #end if
            $opt.high_to_low
            -c '$opt.colour_palette'
    ]]>    </command>
    <inputs>
        <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" />
        <section name="opt" title="Optional arguments" expanded="true">
            <param name="reference" argument="-r" type="text" optional="true" label="Reference sequence (by sequence ID)" help="Indicates which sequence in the alignment is the reference (by sequence ID). Default: first sequence in alignment" />
            <param name="labels" argument="-l" type="data" format="csv" optional="true" label="Labels" help="Optional csv file of labels to show in output snipit plot. Default: sequence names"/>
            <param argument="--l-header" type="text" value="name,label" label="Label headers" help="Comma separated string of column headers in label csv. First field indicates sequence name column, second the label column. Default: 'name,label'" />
            <param name="format" argument="-f" type="select" value="png" label="Output file format" help="Format options. Default: png">
                <option value="png" selected="true">png</option>
                <option value="jpg">jpg</option>
                <option value="pdf">pdf</option>
                <option value="svg">svg</option>
                <option value="tiff">tiff</option>
            </param>
            <param argument="--height" type="float" value="0.0" label="Figure height" help="Overwrite the default figure height." />
            <param argument="--width" type="float" value="0.0" label="Figure width" help="Overwrite the default figure width." />
            <param argument="--size-option" type="select" value="scale" label="Sizing options" help="Specify options for sizing. Options: expand, scale">
                <option value="expand">expand</option>
                <option value="scale" selected="true">scale</option>
            </param>
            <param argument="--flip-vertical" type="boolean" truevalue="--flip-vertical" falsevalue="" value="false" label="Flip plot orientation?" help="Flip the orientation of the plot so sequences are below the reference rather than above it. Default: false" />
            <param argument="--exclude-positions" type="text" optional="true" label="Excluded positions" help="One or more range (closed, inclusive; one-indexed) or specific position to exclude in the output. Ex. '100-150' or Ex. '100 101' Considered after '--include-positions'." />
            <param argument="--exclude-ambig-pos" type="boolean" truevalue="--exclude-ambig-pos" falsevalue="" value="false" label="Exclude ambig positions?" help="Exclude positions with ambig base in any sequences. Considered after '--include-positions'" />
            <param argument="--sort-by-mutation-number" type="boolean" truevalue="--sort-by-mutation-number" falsevalue="" value="false" label="Sort by mutation number?" help="Render the graph with sequences sorted by the number of SNPs relative to the reference (fewest to most). Default: False" />
            <param argument="--sort-by-id" type="boolean" truevalue="--sort-by-id" falsevalue="" value="false" label="Sort by sequence ID?" help="Sort sequences alphabetically by sequence id. Default: False" />
            <param argument="--sort-by-mutations" type="text" optional="true" label="Sort by mutations" help="Sort sequences by bases at specified positions. Positions are comma separated integers. Ex. '1,2,3'" />
            <param argument="--high-to-low" type="boolean" truevalue="--high-to-low" falsevalue="" value="false" label="Sort high to low?" help="If 'sort by mutation number' is selected, show the sequences with the fewest SNPs closest to the reference. Default: False" />
            <param name="colour_palette" argument="-c" type="select" value="classic" label="Colour palette" help="Specify colour palette. Options: primary, classic, purine-pyrimidine, greyscale, wes, verity">
                <option value="primary">primary</option>
                <option value="classic" selected="true">classic</option>
                <option value="purine-pyrimidine">purine-pyrimidine</option>
                <option value="greyscale">greyscale</option>
                <option value="wes">wes</option>
                <option value="verity">verity</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="snp_plot" format="png" label="snp plot" from_work_dir="snp_plot.*">
            <change_format>
                <when input="opt.format" value="jpg" format="jpg" />
                <when input="opt.format" value="pdf" format="pdf" />
                <when input="opt.format" value="svg" format="svg" />
                <when input="opt.format" value="tiff" format="tiff" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="alignment" value="input.fasta" />
            <output name="snp_plot" ftype="png" file="snp_plot.png" compare="sim_size"/>
        </test>
        <test>
            <param name="alignment" value="input.fasta" />
            <param name="reference" value="USA_2" />
            <param name="format" value="pdf" />
            <param name="flip_vertical" value="true" />
            <output name="snp_plot" ftype="pdf" file="snp_plot.pdf" compare="sim_size" />
        </test>
        <test>
            <param name="alignment" value="input.fasta" />
            <param name="format" value="jpg" />
            <param name="colour_palette" value="verity" />
            <output name="snp_plot" ftype="jpg" file="snp_plot.jpg" />
        </test>
        <test>
            <param name="alignment" value="input.fasta" />
            <param name="excluded_positions" value="1-100" />
            <param name="exclude_ambig_pos" value="true" />
            <param name="high_to_low" value="true" />
            <output name="snp_plot" ftype="png" file="snp_plot_ex.png" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Snipit finds the SNPs relative to a reference in a multiple sequence alignment and highlights these changes as a figure.
    ]]>
    </help>
    <citations>
        <citation type="bibtex">
            @UNPUBLISHED{OToole2017,
                author = {O'Toole, Aine},
                title = {snipit: Summarise snps relative to your reference sequence.},
                year = {2017},
                url = {https://github.com/aineniamh/snipit}
            }
        </citation>
    </citations>
</tool>