<macros>
    <token name="@TOOL_VERSION@">4.3.0.1</token>
    <token name="@FUNCTION_BASE@">function['function_select'] == "base"</token>
    <token name="@FUNCTION_CITE@">function['function_select'] == "cite"</token>
    <token name="@VARIABLE_CONTINUE@">function['variable_continue']['variable_continue'] == "yes"</token>
    <token name="@PCA_CONTINUE@">function['variable_continue']['pca_continue']['pca_continue'] == "yes"</token>
    <token name="@CLUSTERS_CONTINUE@">function['variable_continue']['pca_continue']['clusters_continue']['clusters_continue'] == "yes"</token>
    <token name="@MARKERS_CONTINUE@">function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_continue'] == "yes"</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>
            <requirement type="package" version="2.22">r-rmarkdown</requirement>
            <requirement type="package" version="1.14.2">r-data.table</requirement>
        </requirements>
    </xml>
    <xml name="norm" label="Normalizing data" expanded="true">
        <param name="low_thresholds" type="integer" value="1" min="0" label="Low threshold for filtering cells" />
        <param name="high_thresholds" type="integer" value="20000000" min="1" label="High threshold for filtering cells" />
        <param name="vlnfeat"  type="boolean" truevalue="T" falsevalue="F" label="Include violin plot and scatter plot of cell features"/>
        <param name="norm_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after data normalization"/>
    </xml>
    <xml name="variable" label="Variable features" expanded="true">
        <param name="featplot" type="boolean" truevalue="T" falsevalue="F" label="Include plot of variable features"/>
        <param name="var_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after data scaling"/>
    </xml>
    <xml name="pca"  label="Principal component analysis" expanded="true">
        <param name="num_PCs" type="integer" min="0" value="10" label="Number of PCs to use in plots" help="Uses this number of PCs in PCHEatmap, JackStrawPlot, FindClusters, RunTSNE" />
        <param name="pc_plots" type="boolean" truevalue="T" falsevalue="F" label="Include PCA plots"/>
        <param name="pca_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after PCA analysis"/>
    </xml>
    <xml name="clusters" label="Multidimensional scaling and Clustering" expanded="true">
        <param name="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" min="1"/>
        <param name="resolution" type="float" value="0.6" min="0" label="Resolution parameter" help="Value of the resolution parameter used in FindClusters, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities" />
        <param name="nmds" type="boolean" truevalue="T" falsevalue="F" label="Include UMAP and TSNE plots"/>
        <param name="clusters_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after TSNE and UMAP analysis"/>
    </xml>
    <xml name="markers"  label="Marker genes" expanded="true">
        <param name="min_pct" type="float" value="0.1" min="0" max="1.0" label="Minimum percent cells" help="With FindMarkers, only test genes that are detected in at least this percentage of cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed" />
        <param name="logfc_threshold" type="float" min="0" value="0.25" label="Log fold change threshold"
            help="With FindMarkers, limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Increasing this parameter speeds up the function, but can miss weaker signals" />
        <param name="heatmaps" type="boolean" truevalue="T" falsevalue="F" label="Include heatmaps of markers"/>
        <param name="markers_file" type="boolean" truevalue="T" falsevalue="F" label="Output marker data"/>
    </xml>
    <xml name="cite-seq" label="Cite-seq analysis" expanded="true">
        <param name="cite_markers" type="boolean" truevalue="T" falsevalue="F" label="Output list of cite-seq markers"/>
        <conditional name="comparison">
                <param name="comparison" type="select" label="Compare specific feature's effect on protein and rna expression?">
                    <option value="yes">Yes</option>
                    <option value="no" selected="true">No</option>
                </param>
                <when value="yes">
                    <param name="feat_comp" type="text" label="Feature(s) to inspect" help="Comma-separated list of features to directly compare with protein and RNA expression"/>
                </when>
                <when value="no"/>
        </conditional>
        <conditional name="marker_compare">
            <param name="marker_compare" type="select" label="Compare top RNA and protein features graphically against themselves and one another">
                <option value="yes">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes">
                <param name="top_x" type="integer" min="1" value="5" label="How many of the top features should be shown"/>
            </when>
            <when value="no"/>
        </conditional>
    </xml>
</macros>