comparison pcdl_macros.xml @ 0:6d0f91e057f3 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16

0:6d0f91e057f3

<macros>
    <!-- requirements -->
    <xml name="requirement">
        <requirement type="package" version="3.3.8">pcdl</requirement>
    </xml>
    <!-- input -->
    <xml name="aggregate_num">
        <param argument="--aggregate_num" label="aggregation function for focus numeric data" type="select" display="radio" help="">
            <option value="max">max</option>
            <option value="mean" selected="true">mean</option>
            <option value="median">median</option>
            <option value="min">min</option>
            <option value="std">std</option>
            <option value="var">var</option>
        </param>
    </xml>
    <xml name="allvalues">
        <param argument="--allvalues" label="all values" type="boolean" truevalue="true" falsevalue="false" checked="false" help="For numeric data, should only the min and max values or all values be returned?"/>
    </xml>
    <xml name="alpha">
        <param argument="--alpha" label="alpha channel" type="float" value="1.0" optional="false" help="Alpha channel transparency value between 1 (not transparent at all) and 0 (totally transparent)."/>
    </xml>
    <xml name="attribute">
        <param name="attribute" label="attribute" type="text" value="cell_type" optional="false" help="Listing of mcds.get_cell_df dataframe column names, used for cell attributes."/>
    </xml>
    <xml name="cmap">
        <param argument="--cmap" label="color map" type="select" help="Matplotlib colormap from https://matplotlib.org/stable/tutorials/colors/colormaps.html .">
            <!-- perceptually uniform sequential -->
            <option value="viridis" selected="true">viridis</option>
            <option value="viridis_r">viridis reversed</option>
            <option value="plasma">plasma</option>
            <option value="plasma_r">plasma reversed</option>
            <option value="inferno">inferno</option>
            <option value="inferno_r">inferno reversed</option>
            <option value="magam">magma</option>
            <option value="magam_r">magma reversed</option>
            <option value="cividis">cividis</option>
            <option value="cividis_r">cividis reversed</option>
            <!-- sequential -->
            <option value="Greys">Greys</option>
            <option value="Greys_r">Greys reversed</option>
            <option value="Purples">Purples</option>
            <option value="Purples_r">Purples reversed</option>
            <option value="Blues">Blues</option>
            <option value="Blues_r">Blues reversed</option>
            <option value="Greens">Greens</option>
            <option value="Greens_r">Greens reversed</option>
            <option value="Oranges">Oranges</option>
            <option value="Oranges_r">Oranges reversed</option>
            <option value="Reds">Reds</option>
            <option value="Reds_r">Reds reversed</option>
            <option value="YlOrBr">YlOrBr</option>
            <option value="YlOrBr_r">YlOrBr reversed</option>
            <option value="YlOrRd">YlOrRd</option>
            <option value="YlOrRd_r">YlOrRd reversed</option>
            <option value="OrRd">OrRd</option>
            <option value="OrRd_r">OrRd reversed</option>
            <option value="PuRd">PuRd</option>
            <option value="PuRd_r">PuRd reversed</option>
            <option value="RdPu">RdPu</option>
            <option value="RdPu_r">RdPu reversed</option>
            <option value="BuPu">BuPu</option>
            <option value="BuPu_r">BuPu reversed</option>
            <option value="GnBu">GnBu</option>
            <option value="GnBu_r">GnBu reversed</option>
            <option value="PuBu">PuBu</option>
            <option value="PuBu_r">PuBu reversed</option>
            <option value="YlGnBu">YlGnBu</option>
            <option value="YlGnBu_r">YlGnBu reversed</option>
            <option value="PuBuGn">PuBuGn</option>
            <option value="PuBuGn_r">PuBuGn reversed</option>
            <option value="BuGn">BuGn</option>
            <option value="BuGn_r">BuGn reversed</option>
            <option value="YlGn">YlGn</option>
            <option value="YlGn_r">YlGn reversed</option>
            <!-- sequential 2 -->
            <option value="binary">binary</option>
            <option value="binary_r">binary reversed</option>
            <option value="gist_yarg">gist_yarg</option>
            <option value="gist_yarg_r">gist_yarg reversed</option>
            <option value="gist_gray">gist_gray</option>
            <option value="gist_gray_r">gist_gray reversed</option>
            <option value="gray">gray</option>
            <option value="gray_r">gray reversed</option>
            <option value="bone">bone</option>
            <option value="bone_r">bone reversed</option>
            <option value="pink">pink</option>
            <option value="pink_r">pink reversed</option>
            <option value="spring">spring</option>
            <option value="spring_r">spring reversed</option>
            <option value="summer">summer</option>
            <option value="summer_r">summer reversed</option>
            <option value="autumn">autumn</option>
            <option value="autumn_r">autumn reversed</option>
            <option value="winter">winter</option>
            <option value="winter_r">winter reversed</option>
            <option value="cool">cool</option>
            <option value="cool_r">cool reversed</option>
            <option value="Wistia">Wistia</option>
            <option value="Wistia_r">Wistia reversed</option>
            <option value="hot">hot</option>
            <option value="hot_r">hot reversed</option>
            <option value="afmhot">afmhot</option>
            <option value="afmhot_r">afmhot reversed</option>
            <option value="gist_heat">gist_heat</option>
            <option value="gist_heat_r">gist_heat reversed</option>
            <option value="copper">copper</option>
            <option value="copper_r">copper reversed</option>
            <!-- diverging -->
            <option value="PiYG">PiYG</option>
            <option value="PiYG_r">PiYG reversed</option>
            <option value="PRGn">PRGn</option>
            <option value="PRGn_r">PRGn reversed</option>
            <option value="BrBG">BrBG</option>
            <option value="BrBG_r">BrBG reversed</option>
            <option value="PuOr">PuOr</option>
            <option value="PuOr_r">PuOr reversed</option>
            <option value="RdGy">RdGy</option>
            <option value="RdGy_r">RdGy reversed</option>
            <option value="RdBu">RdBu</option>
            <option value="RdBu_r">RdBu reversed</option>
            <option value="RdYlBu">RdYlBu</option>
            <option value="RdYlBu_r">RdYlBu reversed</option>
            <option value="RdYlGn">RdYlGn</option>
            <option value="RdYlGn_r">RdYlGn reversed</option>
            <option value="Spectral">Spectral</option>
            <option value="Spectral_r">Spectral reversed</option>
            <option value="coolwarm">coolwarm</option>
            <option value="coolwarm_r">coolwarm reversed</option>
            <option value="bwr">bwr</option>
            <option value="bwr_r">bwr reversed</option>
            <option value="seismic">seismic</option>
            <option value="seismic_r">seismic reversed</option>
            <option value="berlin">berlin</option>
            <option value="berlin_r">berlin reversed</option>
            <option value="managua">managua</option>
            <option value="managua_r">managua reversed</option>
            <option value="vanimo">vanimo</option>
            <option value="vanimo_r">vanimo reversed</option>
            <!-- cyclic -->
            <option value="twilight">twilight</option>
            <option value="twilight_r">twilight reversed</option>
            <option value="twilight_shifted">twilight_shifted</option>
            <option value="twilight_shifted_r">twilight_shifted reversed</option>
            <option value="hsv">hsv</option>
            <option value="hsv_r">hsv reversed</option>
            <!-- qualitative -->
            <option value="Pastel1">Pastel1</option>
            <option value="Pastel2">Pastel2</option>
            <option value="Paired">Paired</option>
            <option value="Accent">Accent</option>
            <option value="Accent_r">Accent reversed</option>
            <option value="Dark2">Dark2</option>
            <option value="Dark2_r">Dark2 reversed</option>
            <option value="Set1">Set1</option>
            <option value="Set1_r">Set1 reversed</option>
            <option value="Set2">Set2</option>
            <option value="Set2_r">Set2 reversed</option>
            <option value="Set3">Set3</option>
            <option value="Set3_r">Set3 reversed</option>
            <option value="tab10">tab10</option>
            <option value="tab10_r">tab10 reversed</option>
            <option value="tab20">tab20</option>
            <option value="tab20_r">tab20 reversed</option>
            <option value="tab20b">tab20b</option>
            <option value="tab20b_r">tab20b reversed</option>
            <option value="tab20c">tab20c</option>
            <option value="tab20c_r">tab20c reversed</option>
            <!-- miscellaneous -->
            <option value="flag">flag</option>
            <option value="flag_r">flag reversed</option>
            <option value="prism">prism</option>
            <option value="prism_r">prism reversed</option>
            <option value="ocean">ocean</option>
            <option value="ocean_r">ocean reversed</option>
            <option value="gist_earth">gist_earth</option>
            <option value="gist_earth_r">gist_earth reversed</option>
            <option value="terrain">terrain</option>
            <option value="terrain_r">terrain reversed</option>
            <option value="gist_stern">gist_stern</option>
            <option value="gist_stern_r">gist_stern reversed</option>
            <option value="gnuplot">gnuplot</option>
            <option value="gnuplot_r">gnuplot reversed</option>
            <option value="gnuplot2">gnuplot2</option>
            <option value="gnuplot2_r">gnuplot2 reversed</option>
            <option value="CMRmap">CMRmap</option>
            <option value="CMRmap_r">CMRmap reversed</option>
            <option value="cubehelix">cubehelix</option>
            <option value="cubehelix_r">cubehelix reversed</option>
            <option value="brg">brg</option>
            <option value="brg_r">brg reversed</option>
            <option value="gist_rainbow">gist_rainbow</option>
            <option value="gist_rainbow_r">gist_rainbow reversed</option>
            <option value="rainbow">rainbow</option>
            <option value="rainbow_r">rainbow reversed</option>
            <option value="jet">jet</option>
            <option value="jet_r">jet reversed</option>
            <option value="turbo">turbo</option>
            <option value="turbo_r">turbo reverse</option>
            <option value="gist_ncar">gist_ncar</option>
            <option value="gist_ncar_r">gist_ncar reversed</option>
        </param>
    </xml>
    <xml name="collapse">
        <param argument="--collapse" label="collapse" type="boolean" truevalue="true" falsevalue="false" checked="true" help="Should all mcds time steps from the time series be collapsed into one big file, or a many files, one file for each time step?"/>
    </xml>
    <xml name="color">
        <param argument="--color" label="color" type="text" value="none" optional="false" help="Listing of color strings referred to by name, RGB or RGBA code."/>
    </xml>
    <xml name="custom_data_type">
        <param argument="--custom_data_type" label="custom data type" type="text" value="" optional="true" help="Parameter to specify custom_data variable types other than float (namely: int, bool, str) like this var:dtype myint:int mybool:bool mystr:str. Downstream float and int will be handled as numeric, bool as Boolean, and str as categorical data."/>
    </xml>
    <xml name="drop">
        <param argument="--drop" label="drop" type="text" value="" optional="true" help="Set of column labels (pcdl_get_cell_attribute_list, pcdl_get_substrate_list) to be dropped. Don't worry: essential columns like ID, coordinates and time will never be dropped. Attention: when the keep parameter is given, then the drop parameter has to be an empty string!"/>
    </xml>
    <xml name="edge_attribute">
        <param argument="--edge_attribute" label="edge attribute" type="boolean" truevalue="true" falsevalue="false" checked="true" help="Specifies if the spatial Euclidean distance is used for edge attribute, to generate a weighted graph."/>
    </xml>
    <xml name="entropy">
        <param name="entropy" label="values" type="integer" value="1" optional="false" help="Minimal number of values a variable has to have in any of the mcds time steps to be outputted. Variables that have only 1 state carry no information. None is a state too."/>
    </xml>
    <xml name="ext">
        <param argument="--ext" label="file extension" type="select" display="radio" help="Output image format. Possible formats are jpeg, png, and tiff.">
            <option value="jpeg" selected="true">jpeg</option>
            <!--
        <option value="png">png</option>
        <option value="tiff">tiff</option>
        -->
        </param>
    </xml>
    <xml name="extrema">
        <param argument="--extrema" label="extrem values" type="text" value="none" optional="false" help="Two floats separated by a space. None takes min and max from data.">
            <validator type="regex" message="None or two float values separated by a space!">^[enoENO0-9-. ]*$</validator>
        </param>
    </xml>
    <xml name="figbgcolor">
        <param argument="--figbgcolor" label="figure background color" type="text" value="none" optional="false" help="Figure background color. None is transparent (png) or white (jpeg, tiff)."/>
    </xml>
    <xml name="figsizepx_x">
        <param name="figsizepx_x" label="figure size x-axis in pixel" type="integer" value="640" optional="false" help="Size of the figure in pixels. The given x and y will be rounded to the nearest even number, to be able to generate movies from the images. (--figsizepx)"/>
    </xml>
    <xml name="figsizepx_y">
        <param name="figsizepx_y" label="figure size y-axis in pixel" type="integer" value="480" optional="false" help="Size of the figure in pixels. The given x and y will be rounded to the nearest even number, to be able to generate movies from the images. (--figsizepx)"/>
    </xml>
    <xml name="fill">
        <param argument="--fill" label="fill" type="boolean" truevalue="true" falsevalue="false" checked="true" help="True generates a matplotlib contourf plot. False generates a matplotlib contour plot."/>
    </xml>
    <xml name="focus_cell">
        <param name="focus_cell" label="focus" type="text" value="cell_type" optional="false" help="Column name from the pcdl_get_cell_attribute_list listing."/>
    </xml>
    <xml name="focus_subs">
        <param name="focus_subs" label="focus" type="text" optional="false" help="Substrate from the pcdl_get_substrate_list listing."/>
    </xml>
    <xml name="focus_cat">
        <param name="focus_cat" label="focus categorical data" type="text" value="none" optional="false" help="Categorical or boolean data column within dataframe specified under frame (pcdl_get_cell_attribute_list or pcdl_get_substrate_list). None is total, which is all agents or voxels, no categories."/>
    </xml>
    <xml name="focus_num">
        <param name="focus_num" label="focus numerical data" type="text" value="none" optional="false" help="Numerical data column within dataframe specified under frame (pcdl_get_cell_attribute_list or pcdl_get_substrate_list). None is count, agent or voxel count."/>
    </xml>
    <xml name="frame">
        <param argument="--frame" label="frame" type="select" display="radio" help="To specifies the data dataframe from which the values are taken. Cell: agent centric value. Conc: whole domain centric substarte concentration values.">
            <option value="cell" selected="true">cell</option>
            <option value="conc">conc</option>
        </param>
    </xml>
    <xml name="framerate">
        <param argument="--framerate" label="values" type="integer" value="12" optional="false" help="Specifies how many images per second will be used. Humans are capable of processing 12 images per second and seeing them individually. Higher rates are seen as motion."/>
    </xml>
    <xml name="graph">
        <param argument="--graph" label="graph" type="boolean" truevalue="true" falsevalue="false" checked="true" help="Should neighbor graph, attached graph, and attached spring graph be extracted and loaded into the resulting object?"/>
    </xml>
    <xml name="graph_type">
        <param argument="--graph_type" label="graph type" type="select" display="radio" help="Specify which physicell graph output data should be processed. Neighbor: neighbor graph data. Attached: attached graph data. Spring: spring attache graph data.">
            <option value="neighbor" selected="true">neighbor</option>
            <option value="attached">attached</option>
            <option value="spring">spring</option>
        </param>
    </xml>
    <xml name="grid">
        <param argument="--grid" label="grid" type="boolean" truevalue="true" falsevalue="false" checked="true" help="Plot axis grid lines."/>
    </xml>
    <xml name="interface">
        <param name="interface" label="interface" type="select" display="radio" help="Specify the image format from which the gif will be generated. These images can be generated with the pcdl_plot_scatter or pcdl_plot_contour function.">
            <option value="jpeg" selected="true">jpeg</option>
            <!--
        <option value="png">png</option>
        <option value="tiff">tiff</option>
        -->
        </param>
    </xml>
    <xml name="keep">
        <param argument="--keep" label="keep" type="text" value="" optional="true" help="Set of column labels (pcdl_get_cell_attribute_list, pcdl_get_substrate_list) to be kept. Set parameter values to 1 to be sure that all variables are kept. Don't worry: essential columns like ID, coordinates and time will always be kept."/>
    </xml>
    <xml name="legend">
        <param argument="--legend" label="legend" type="select" display="radio" help="If True or reverse, place legend on axis subplots.">
            <option value="false">false</option>
            <option value="reverse">reverse</option>
            <option value="true" selected="true">true</option>
        </param>
    </xml>
    <xml name="legend_loc">
        <param argument="--legend_loc" label="legend location" type="select" display="radio" help="The location of the categorical legend, if applicable.">
            <option value="best">best</option>
            <option value="upper right">upper right</option>
            <option value="upper center"/>
            <option value="upper left"/>
            <option value="center left"/>
            <option value="lower left" selected="true"/>
            <option value="lower center"/>
            <option value="lower right"/>
            <option value="center right"/>
            <option value="center"/>
        </param>
    </xml>
    <xml name="linestyle">
        <param argument="--linestyle" label="line style" type="select" display="radio" help="Matplotlib line style.">
            <option value="-" selected="true">-</option>
            <option value="--">--</option>
            <option value=".-">.-</option>
            <option value=":">:</option>
        </param>
    </xml>
    <xml name="linewidth">
        <param argument="--linewidth" label="line width" type="integer" value="1" optional="false" help="Line width in points."/>
    </xml>
    <xml name="logy">
        <param argument="--logy" label="logarithmic y-axis" type="boolean" truevalue="true" falsevalue="false" checked="false" help="If True, then y axis is natural log scaled."/>
    </xml>
    <xml name="microenv">
        <param argument="--microenv" label="micro environment" type="boolean" truevalue="true" falsevalue="false" checked="true" help="Should the microenvironment be extracted and loaded into the resulting object? Setting microenv to False will use less memory and speed up processing."/>
    </xml>
    <xml name="node_attribute">
        <param argument="--node_attribute" label="node attribute" type="text" value="" optional="true" help="Listing of pcdl_get_cell_attribute attributes, used for node attributes."/>
    </xml>
    <xml name="path">
        <param name="path" label="data collection" type="data_collection" collection_type="list" help="PhysiCell output data collection."/>
    </xml>
    <xml name="physiboss">
        <param argument="--physiboss" label="physiboss" type="boolean" truevalue="true" falsevalue="false" checked="true" help="If found, should physiboss state data be extracted and loaded into the resulting object?"/>
    </xml>
    <xml name="s">
        <param argument="--s" label="s" type="float" value="1.0" optional="false" help="Scatter plot dot size scale factor. With figsizepx extracted from initial.svg, scale factor 1.0 should be ok. Adjust if necessary."/>
    </xml>
    <xml name="scale">
        <param argument="--scale" label="scale" type="select" display="radio" help="Specify how the data should be scaled. Possible values are None, maxabs, minmax, std. None: no scaling. Maxabs: maximum absolute value distance scaler maps all values linearly into a [-1, 1] interval. Minmax: minimum maximum distance scaler maps all values linearly into a [0, 1] interval. Std: standard deviation scaler maps all values to sigmas.">
            <option value="none">none</option>
            <option value="maxabs" selected="true">maxabs</option>
            <option value="minmax">minmax</option>
            <option value="std">std</option>
        </param>
    </xml>
    <xml name="secondary_y">
        <param argument="--secondary_y" label="secondary y-axis" type="boolean" truevalue="true" falsevalue="false" checked="false" help="Plot on the secondary y-axis?"/>
    </xml>
    <xml name="sharex">
        <param argument="--sharex" label="shared x-axis" type="boolean" truevalue="true" falsevalue="false" checked="false" help="In case subplots is True, share x-axis by setting some x-axis labels to invisible."/>
    </xml>
    <xml name="sharey">
        <param argument="sharey" label="shared y-axis" type="boolean" truevalue="true" falsevalue="false" checked="false" help="In case subplots is True, share y-axis range and possibly setting some y-axis labels to invisible."/>
    </xml>
    <xml name="subplots">
        <param argument="--subplots" label="subplots" type="boolean" truevalue="true" falsevalue="false" checked="false" help="`Should the plot be split into subplots, one per curve?"/>
    </xml>
    <xml name="title">
        <param argument="--title" label="title" type="text" value="none" optional="false" help="Title to use for the plot. None will print no title."/>
    </xml>
    <xml name="title_prefix.">
        <param argument="--title_prefix" label="title" type="text" value="" optional="true" help="Title prefix."/>
    </xml>
    <xml name="verbose">
        <param argument="--verbose" label="verbose" type="boolean" truevalue="true" falsevalue="false" checked="false" help="Setting verbose to True for more text output, while processing."/>
    </xml>
    <xml name="xlim">
        <param argument="--xlim" label="x-axis limit" type="text" value="none" optional="false" help="Two floats separated by a space. X axis min and max value. None takes min and max from mesh x axis range.">
            <validator type="regex" message="None or two float values separated by a space!">^[enoENO0-9-. ]*$</validator>
        </param>
    </xml>
    <xml name="xyequal">
        <param argument="--xyequal" label="equal x-axis y-axis spacing" type="boolean" truevalue="true" falsevalue="false" checked="true" help="To specify equal axis spacing for x and y axis."/>
    </xml>
    <xml name="ylim">
        <param argument="--ylim" label="y-axis limit" type="text" value="none" optional="false" help="Two floats separated by a space. y axis min and max value. None takes min and max from mesh y axis range.">
            <validator type="regex" message="None or two float values separated by a space!">^[enoENO0-9-. ]*$</validator>
        </param>
    </xml>
    <xml name="yunit">
        <param argument="--yunit" label="y-axis unit" type="text" value="none" optional="false" help="String to specify y-axis unit. None will not print a unit on the y-axis."/>
    </xml>
    <xml name="z_axis">
        <param argument="--z_axis" label="z-axis" type="text" value="none" optional="false" help="For a categorical focus: list of labels; for a numeric focus: list of two floats; None, depending on the focus column variable dtype, extracts labels or min and max values from data."/>
    </xml>
    <xml name="z_slice">
        <param argument="--z_slice" label="z-axis slice" type="float" value="0.0" optional="false" help="Z-axis cut position to slice a 2D xy-plain out of the 3D mesh. If z_slice position numeric but not an exact mesh center coordinate, then z_slice will be adjusted to the nearest mesh center value, the smaller one, if the coordinate lies on a saddle point."/>
    </xml>
    <!-- test -->
    <xml name="output">
        <collection type="list">
            <element name="initial_attached_cells_graph.txt" value="initial_attached_cells_graph.txt"/>
            <element name="initial_cell_neighbor_graph.txt" value="initial_cell_neighbor_graph.txt"/>
            <element name="initial_cells.mat" value="initial_cells.mat"/>
            <element name="initial_mesh0.mat" value="initial_mesh0.mat"/>
            <element name="initial_microenvironment0.mat" value="initial_microenvironment0.mat"/>
            <element name="initial_spring_attached_cells_graph.txt" value="initial_spring_attached_cells_graph.txt"/>
            <element name="initial.svg" value="initial.svg"/>
            <element name="initial.xml" value="initial.xml"/>
            <element name="legend.svg" value="legend.svg"/>
            <element name="output00000000_attached_cells_graph.txt" value="output00000000_attached_cells_graph.txt"/>
            <element name="output00000000_cell_neighbor_graph.txt" value="output00000000_cell_neighbor_graph.txt"/>
            <element name="output00000000_cells.mat" value="output00000000_cells.mat"/>
            <element name="output00000000_microenvironment0.mat" value="output00000000_microenvironment0.mat"/>
            <element name="output00000000_spring_attached_cells_graph.txt" value="output00000000_spring_attached_cells_graph.txt"/>
            <element name="output00000000.xml" value="output00000000.xml"/>
            <element name="output00000001_attached_cells_graph.txt" value="output00000001_attached_cells_graph.txt"/>
            <element name="output00000001_cell_neighbor_graph.txt" value="output00000001_cell_neighbor_graph.txt"/>
            <element name="output00000001_cells.mat" value="output00000001_cells.mat"/>
            <element name="output00000001_microenvironment0.mat" value="output00000001_microenvironment0.mat"/>
            <element name="output00000001_spring_attached_cells_graph.txt" value="output00000001_spring_attached_cells_graph.txt"/>
            <element name="output00000001.xml" value="output00000001.xml"/>
            <element name="final_attached_cells_graph.txt" value="final_attached_cells_graph.txt"/>
            <element name="final_cell_neighbor_graph.txt" value="final_cell_neighbor_graph.txt"/>
            <element name="final_cells.mat" value="final_cells.mat"/>
            <element name="final_microenvironment0.mat" value="final_microenvironment0.mat"/>
            <element name="final_spring_attached_cells_graph.txt" value="final_spring_attached_cells_graph.txt"/>
            <element name="final.svg" value="final.svg"/>
            <element name="final.xml" value="final.xml"/>
            <element name="PhysiCell_settings.xml" value="PhysiCell_settings.xml"/>
            <!-- test pcdl_make_gif.xml and pcdl_make_movie.xml -->
            <element name="output00000000_oxygen.jpeg" value="output00000000_oxygen.jpeg"/>
            <element name="output00000001_oxygen.jpeg" value="output00000001_oxygen.jpeg"/>
        </collection>
    </xml>
    <!-- meta -->
    <xml name="citation">
        <citation type="bibtex">
        @misc{githubphysicelldataloader,
            author = {Bucher, Elmar},
            year = {2025},
            title = {physicelldataloader},
            publisher = {GitHub},
            journal = {GitHub repository},
            url = {https://github.com/elmbeech/physicelldataloader},
        }</citation>
    </xml>
</macros>