annotate bandage_image.xml @ 8:ddddce450736 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 2b3b163bbe36bb648c17c9b0bf808d41d92078c0

<tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy4" profile="21.05">
    <description>visualize de novo assembly graphs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"> <![CDATA[

ln -s '$input_file' input.gfa &&

@HEADLESS@
Bandage
    image
    input.gfa
    'out.$output_format'
    #if $height:
        --height '$height'
    #end if
    #if $width:
        --width '$width'
    #end if
    #if $fontsize:
        --fontsize '$fontsize'
    #end if
    #if $nodewidth:
        --nodewidth '$nodewidth'
    #end if
    $names
    $lengths
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="gfa1,gfa2,fastg,txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
        <param argument="--height" type="integer" min="1" value="1000" optional="True" label="Image height" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: 1000."/>
        <param argument="--width" type="integer" min="1" optional="True" label="Image width" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: not set."/>
        <param argument="--names" type="boolean" truevalue="--names" falsevalue="" label="Node name labels?"/>
        <param argument="--lengths" type="boolean" truevalue="--lengths" falsevalue="" label="Node length labels?"/>
        <param argument="--fontsize" type="integer" min="5" optional="true" label="Font size" help="Node font size?"/>
        <param argument="--nodewidth" type="float" min="5" optional="true" label="Node width" help="Node width for graph image?" />
        <param name="output_format" type="select" label="Produce jpg, png or svg file?">
            <option selected="True" value="jpg">.jpg</option>
            <option value="png">.png</option>
            <option value="svg">.svg</option>
        </param>

    </inputs>
    <outputs>
        <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image">
            <change_format>
                <when input="output_format" value="png" format="png"/>
                <when input="output_format" value="svg" format="svg"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test><!-- test with default settings -->
            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
            <output name="outfile" ftype="jpg">
              <assert_contents>
                  <has_size value="47168" delta="15000"/>
              </assert_contents>
            </output>
        </test>
        <test><!-- test with width and height parameters -->
            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
            <param name="height" value="100"/>
            <param name="width" value="100"/>
            <param name="output_format" value="png"/>
            <output name="outfile" ftype="png">
              <assert_contents>
                  <has_size value="2000" delta="1500"/>
              </assert_contents>
            </output>
        </test>
        <test><!-- test svg output -->
            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
            <param name="output_format" value="svg"/>
            <output name="outfile" ftype="svg">
              <assert_contents>
                  <has_size value="15154" delta="5000"/>
              </assert_contents>
            </output>
        </test>
        <test><!-- test with node name and length labels -->
            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
            <param name="output_format" value="svg"/>
            <param name="names" value="--names"/>
            <param name="lengths" value="--lengths"/>
            <output name="outfile" ftype="svg">
              <assert_contents>
                  <has_size value="49566" delta="15000"/>
              </assert_contents>
            </output>
        </test>
        <test><!-- test with node name, length labels and fontsize-->
            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
            <param name="output_format" value="jpg"/>
            <param name="names" value="--names"/>
            <param name="lengths" value="--lengths"/>
            <param name="fontsize" value="5"/>
            <output name="outfile" ftype="jpg">
              <assert_contents>
                  <has_size value="45286" delta="15000"/>
              </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

*THE NEW BANDAGE: As of version 2022.09, the Bandage tool is now built on `Bandage-NG <https://github.com/asl/BandageNG>`_. This fork of the original Bandage is better maintained with additional features and performance upgrades.*

@BANDAGE_OVERVIEW@

**Command Documentation**

``Bandage image`` will generate an image file of the graph visualisation.

.. image:: $PATH_TO_IMAGES/bandage_graph.png
   :alt: example bandage plot

    ]]></help>
    <expand macro="citations"/>
</tool>