annotate seurat_hover_locator.xml @ 0:60e3b8960913 draft default tip

planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6

<tool id="seurat_hover_locator" name="Seurat Hover Locator" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
    <description>produces an interactive plot with data overlay</description>
    <macros>
        <import>seurat_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version" />
    <command detect_errors="exit_code"><![CDATA[
    seurat-hover-locator.R

    --plot-rds '$plot_rds'


    #if $information_table
    --information-table '$information_table'
    #end if

    $stringsAsFactors


    #if $key
    --key '$key'
    #end if

    $keepLeadingZeros

    $axes

    $dark_theme


    --output-html '$output_html'

    $selfcontained


    #if $libdir
    --libdir '$libdir'
    #end if

    
    ]]></command>
    <inputs>
        <param label="RDS with ggplot2 object from Seurat 4"  name="plot_rds" argument="--plot-rds" type="data" format='?'  help="None"/>
        <param label="Information-table" optional='true' name="information_table" argument="--information-table" type="data" format='txt,tabular,csv'  help="Table with information for overlaying on the plot. Usually the result of calling FetchData on the original Seurat object."/>
        <param label="Stringsasfactors" optional='true' value='true' name="stringsAsFactors" argument="--do-not-stringsAsFactors" type="boolean"  truevalue='' falsevalue='--do-not-stringsAsFactors' checked='true' help="Load strings as factors."/>
        <param label="Key" optional='true' name="key" argument="--key" type="text"   help="Key (index) for the information table"/>
        <param label="Keepleadingzeros" optional='true' value='true' name="keepLeadingZeros" argument="--do-not-keepLeadingZeros" type="boolean"  truevalue='' falsevalue='--do-not-keepLeadingZeros' checked='true' help="If TRUE a column containing numeric data with leading zeros will be read as character, otherwise leading zeros will be removed and converted to numeric."/>
        <param label="Axes" optional='true' value='true' name="axes" argument="--do-not-axes" type="boolean"  truevalue='' falsevalue='--do-not-axes' checked='true' help="Display x- and y-axes"/>
        <param label="Dark theme" optional='true' value='false' name="dark_theme" argument="--dark-theme" type="boolean"  truevalue='--dark-theme' falsevalue='' checked='false' help="Plot using a dark theme?"/>
        <param label="Selfcontained" optional='true' value='true' name="selfcontained" argument="--do-not-selfcontained" type="boolean"  truevalue='' falsevalue='--do-not-selfcontained' checked='true' help="Whether to save the HTML as a single self-contained file (with external resources base64 encoded) or a file with external resources placed in an adjacent directory."/>
        <param label="Libdir" optional='true' name="libdir" argument="--libdir" type="text"   help="Directory to copy HTML dependencies into (defaults to filename_files)."/>
 
    </inputs>
    <outputs>
        <data label="${tool.name} on ${on_string}: Output-html" name="output_html" format='html' />
    </outputs>
    <tests>
 
    </tests>            
<help>
 
</help>            
    <expand macro="citations" />
</tool>