plot_clusters_prevalence.xml

<tool id="plot_cellular_prevalence" name="Cluster Prevalence Over Samples" version="1.0">
    <description>
        Plot the prevalence of clusters over sample from the TSV output of PyClone-VI.
    </description>
    <requirements>
        <requirement type="package" version="1.2.5">pandas</requirement>
        <requirement type="package" version="3.4.3">matplotlib</requirement>
        <requirement type="package" version="0.11.2">seaborn</requirement>
    </requirements>
    <command interpreter="python">
        #set $timepoints_str = ",".join(["%s,%s" % (tp['event_id'], tp['start_date']) for tp in $timepoints])
        ${__tool_directory__}/plot_clusters_prevalence.py --input_file "$input_file" --timepoints "$timepoints_str"
    </command>
    <environment_variables>
        <environment_variable name="MPLCONFIGDIR">${__tool_directory__}/mpl_config</environment_variable>
    </environment_variables>
    <inputs>
        <param name="input_file" type="data" format="tabular" label="Input File"/>
        <repeat name="timepoints" title="Annotate timepoint" help="Annotate every timepoints of experiments. Timepoints without annotation will not be plotted!!" min="1">
            <param name="event_id" type="text" label="Event ID" help="Must match an ID from the Pyclone-VI TSV output" optional="false" />
            <param name="start_date" type="text" label="Start Date" help="In days from the start point/birth" optional="false" />
        </repeat>
    </inputs>
    <outputs>
        <data format="png" name="output_file" from_work_dir="output.png" label="${tool.name}_on_${on_string}.png"/>
    </outputs>
    <help>
        This tool plots cluster prevalence over samples from PyClone-VI tabular output.
    </help>
</tool>