annotate vis.xml @ 2:911a3517b738 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 7704c7c172c1c511dc23a3e5babdf3bf8e5198eb

<tool id="odgi_viz" name="odgi viz" version="@TOOL_VERSION@">
    <description>variation graph visualizations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
odgi viz
-i '$input'
--out='$output'
-x $width
-y $height
#if str($path_height)
    --path-height=$path_height
#end if
#if str($path_x_padding)
    --path-x-padding=$path_x_padding
#end if
$path_per_row
#if str($link_path_pieces):
    --link-path-pieces=$link_path_pieces
#end if
--threads=\${GALAXY_SLOTS:-1}
    ]]></command>
    <inputs>
        <param name="input" type="data" format="odgi" label="odgi input file" />

        <param argument="--width" type="integer" min="0" value="4000" label="Width in pixels of output image" />
        <param argument="--height" type="integer" min="0" value="500" label="Height in pixels of output image" />

        <param argument="--path-height" type="integer" min="0" optional="true" label="Path display height" />
        <param argument="--path-x-padding" type="integer" min="0" optional="true" label="Path x padding" />
        <param argument="--path-per-row" type="boolean" truevalue="--path-per-row" falsevalue=""
            label="Display a single path per row rather than packing them" />

        <param argument="--link-path-pieces" type="float" optional="true"
            label="Show thin links of this relative width to connect path pieces" />
    </inputs>
    <outputs>
        <data name="output" format="png" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="note5_out.og" ftype="odgi" />
            <param name="width" value="4000" />
            <param name="height" value="500" />
            <output name="output" file="note5.png" ftype="png" />
        </test>
    </tests>
    <help><![CDATA[
optimized dynamic genome/graph implementation (odgi)
----------------------------------------------------

variation graph visualizations (viz)
    ]]></help>
    <expand macro="citations" />
</tool>