view graphlan.xml @ 0:c5746c07ca5e draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty

<tool id="graphlan" name="GraPhlAn" version="0.1.0">

    <description>to produce graphical output of an input tree</description>

    <requirements>
        <requirement type="package" version="1.66">biopython</requirement>
        <requirement type="package" version="1.4">matplotlib</requirement>
        <requirement type="package" version="1.0">graphlan</requirement>
    </requirements>

    <stdio>
    </stdio>

    <version_command>
<![CDATA[
python \${GRAPHLAN_DIR}/graphlan.py -v
]]>
    </version_command>

    <command>
<![CDATA[        
        python \${GRAPHLAN_DIR}/graphlan.py
            --format $format

            #if $dpi
                --dpi $dpi
            #end if

            --size $size

            #if $pad
                --pad $pad
            #end if

            $input_tree

            #if str($format) == "png"
                $png_output_image
            #else if str($format) == "pdf"
                $pdf_output_image
            #else if str($format) == "ps"
                $ps_output_image
            #else if str($format) == "eps"
                $eps_output_image
            #else
                $svg_output_image
            #end if
]]>
    </command>

    <inputs>
        <param name="input_tree" type="data" format="txt" label="Input tree in 
            PhlyloXML format" help=""/>

        <param name='format' type="select" label="Output format"
            help="(--format)">
            <option value="png" selected="true">PNG</option>
            <option value="pdf">PDF</option>
            <option value="ps">PS</option>
            <option value="eps">EPS</option>
            <option value="svg">SVG</option>
        </param>

        <param name="dpi" type="integer" label="Dpi of the output image
            (Optional)" help="For non vectorial formats (--dpi)" optional="True"/>

        <param name="size" type="integer" value="7" label="Size of the output image
            (in inches)" help="(--size)"/>

        <param name="pad" type="integer" label="Distance between the most external 
            graphical element and the border of the image (Optional)" 
            help="(--pad)" optional="True"/>
    </inputs>

    <outputs>
        <data format="png" name="png_output_image" 
            label="${tool.name} on ${on_string}: Image">
            <filter>format=="png"</filter>
        </data>
        <data format="pdf" name="pdf_output_image" 
            label="${tool.name} on ${on_string}: Image">
            <filter>format=="pdf"</filter>
        </data>
        <data format="ps" name="ps_output_image" 
            label="${tool.name} on ${on_string}: Image">
            <filter>format=="ps"</filter>
        </data>
        <data format="eps" name="eps_output_image" 
            label="${tool.name} on ${on_string}: Image">
            <filter>format=="eps"</filter>
        </data>
        <data format="svg" name="svg_output_image" 
            label="${tool.name} on ${on_string}: Image">
            <filter>format=="svg"</filter>
        </data>
    </outputs>

    <tests>
        <test>
        </test>
    </tests>

    <help><![CDATA[

**What it does**

GraPhlAn is a software tool for producing high-quality circular 
representations of taxonomic and phylogenetic trees. GraPhlAn focuses on 
concise, integrative, informative, and publication-ready representations of 
phylogenetically- and taxonomically-driven investigation.

For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.

    ]]></help>

    <citations>
    </citations>
</tool>