annotate graphlan.xml @ 0:83baf73b0e79 draft default tip

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty

<tool id="graphlan" name="GraPhlAn" version="0.9.7">

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

    <macros>
        <import>graphlan_macros.xml</import>
    </macros>

    <expand macro="requirements"/>

    <stdio>
        <regex match="Warning"
               source="stderr"
               level="warning"
               description="" />
    </stdio>

    <version_command>
<![CDATA[
graphlan.py -v
]]>
    </version_command>

    <command>
<![CDATA[        
        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" help="The tree must be in PhlyloXML, Newick or text format."/>

        <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>
            <param name="input_tree" value="intermediary_tree.txt"/>
            <param name="format" value="png"/>
            <param name="dpi" value="100"/>
            <param name="size" value="7"/>
            <param name="pad" value="2"/>
            <output name="png_output_image" file="png_image.png" />
        </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>