comparison bandage_image.xml @ 4:94fe43e75ddc draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 585f5fa2d2714638c84b3c9ddaeb5a9557159a95"

3:b2860df42e16

<tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy2" profile="18.01">
    <description>visualize de novo assembly graphs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        --height '$height'
    #end if
    #if $width:
        --width '$width'
    #end if
    $names
    $lengths
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="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 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>

            <param name="output_format" value="svg"/>
            <param name="names" value="--names"/>
            <param name="lengths" value="--lengths"/>
            <output name="outfile" ftype="svg" file="out_labels.svg" compare="sim_size" delta="250000"/>
        </test>
    </tests>
    <help><![CDATA[
@BANDAGE_OVERVIEW@

**Command Documentation**

4:94fe43e75ddc

<tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy3" profile="18.01">
    <description>visualize de novo assembly graphs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        --height '$height'
    #end if
    #if $width:
        --width '$width'
    #end if
    #if $fontsize:
        --fontsize '$fontsize'
    #end if
    $names
    $lengths
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="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 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>

            <param name="output_format" value="svg"/>
            <param name="names" value="--names"/>
            <param name="lengths" value="--lengths"/>
            <output name="outfile" ftype="svg" file="out_labels.svg" compare="sim_size" delta="250000"/>
        </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" file="out_fontsize.jpg" compare="sim_size" delta="250000"/>
        </test>
    </tests>
    <help><![CDATA[
@BANDAGE_OVERVIEW@

**Command Documentation**