<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy0">
    <description>- toolkit for exploration of single-cell RNA-seq data</description>
    <macros>
        <token name="@TOOL_VERSION@">4.3.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>
        <requirement type="package" version="2.18">r-rmarkdown</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#if "vln" in $meta.plots:
    #set $vln = 'T'
#else
    #set $vln = 'F'
#end if
#if "feat" in $meta.plots:
    #set $feat = 'T'
#else
    #set $feat = 'F'
#end if
#if "PCs" in $meta.plots:
    #set $PCs = 'T'
#else
    #set $PCs = 'F'
#end if
#if "tsne" in $meta.plots:
    #set $tsne = 'T'
#else
    #set $tsne = 'F'
#end if
#if "heat" in $meta.plots:
    #set $heatmaps = 'T'
#else
    #set $heatmaps = 'F'
#end if
#if not str($adv.perplexity):
    #set $adv_perplexity = -1
#else:
    #set $adv_perplexity = $adv.perplexity
#end if
Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\",
    params = list(counts = \"${counts}\",
        min_cells = \"${adv.min_cells}\",
        min_genes = \"${adv.min_genes}\",
        low_thresholds = \"${adv.low_thresholds}\",
        high_thresholds = \"${adv.high_thresholds}\",
        numPCs = \"${adv.num_PCs}\",
        cells_use = \"${adv.cells_use}\",
        resolution = \"${adv.resolution}\",
        perplexity = \"${adv_perplexity}\",
        min_pct = \"${adv.min_pct}\",
        logfc_threshold = \"${adv.logfc_threshold}\",
        warn = \"${meta.warn}\",
        varstate = \"${meta.varstate}\",
        showcode = \"${meta.showcode}\",
        vlnfeat = \"$vln\",
        featplot = \"$feat\",
        PCplots = \"$PCs\",
        tsne = \"$tsne\",
        heatmaps = \"$heatmaps\"),
    intermediates_dir = \".\",
    output_format = html_document(),
    output_dir = \".\",
    output_file = \"out.html\")"
    ]]></command>
    <inputs>
        <param name="counts" type="data" format="tabular,tsv" label="Counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/>
        <section name="adv" title="Advanced Options" 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="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" />
            <param name="min_genes" type="integer" min="0"  value="0" label="Minimum genes" help="Include cells where at least this many genes are detected" />
            <param name="low_thresholds" type="integer" value="1" label="Low threshold for filtering cells" />
            <param name="high_thresholds" type="integer" value="20000000" label="High threshold for filtering cells" />
            <param name="cells_use" type="integer" min="1" value="500" label="Cells to use for PCHeatmap" help="Plots this number of top ‘extreme’ cells on both ends of the spectrum, which dramatically speeds plotting for large datasets" />
            <param name="resolution" type="float" value="0.6" 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="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" />
            <param name="min_pct" type="float" value="0.1" 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" />
        </section>
        <section name="meta" title="Output options" expanded="true">
            <param name="showcode" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Show code alongside outputs?"/>
            <param name="warn" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Include warnings in the output file (Yes) or pipe to stdout (No)"/>
            <param name="varstate" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Display variable values used in code at the beginning of output file?"/>
            <param name="plots" type="select" optional="true" multiple="true" display="checkboxes" label="Which plots should be output?">
                <option value="vln" selected="true">Violin and Scatter plots</option>
                <option value="feat" selected="true">Feature counts plots</option>
                <option value="PCs" selected="true">PC plots</option>
                <option value="tsne" selected="true">tSNE plots</option>
                <option value="heat" selected="true">Heatmap plots</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="out_html" format="html" from_work_dir="out.html" label="${tool.name} on ${on_string}" />
    </outputs>

    <tests>
        <test>
            <param name="counts" ftype="tabular" value="counts.tab.gz"/>
            <section name="adv">
                <param name="numPCs" value="10" />
                <param name="min_cells" value="3"/>
                <param name="min_genes" value="200"/>
                <param name="low_thresholds" value="1" />
                <param name="high_thresholds" value="20000000" />
                <param name="cells_use" value="500"/>
                <param name="resolution" value="0.6" />
                <param name="min_pct" value="0.25" />
                <param name="logfc_threshold" value="0.25" />
            </section>
            <section name="meta">
                <param name="showcode" value="T"/>
                <param name="warn" value="F"/>
                <param name="varstate" value="F"/>
                <param name="plots" value="feat"/>
            </section>
            <output name="out_html" ftype="html">
                <assert_contents>
                    <has_text text="Seurat Analysis" />
                    <has_text text="Performed using Galaxy" />
                    <has_text text="img src=&quot;data:image/png;base64" />
                </assert_contents>
            </output>
        </test>
        <test> <!-- perplexity test -->
            <param name="counts" ftype="tabular" value="counts.tab.gz"/>
            <section name="adv">
                <param name="numPCs" value="10" />
                <param name="min_cells" value="3"/>
                <param name="min_genes" value="200"/>
                <param name="low_thresholds" value="1" />
                <param name="high_thresholds" value="20000000" />
                <param name="cells_use" value="500"/>
                <param name="resolution" value="0.6" />
                <param name="perplexity" value="16" />
                <param name="min_pct" value="0.25" />
                <param name="logfc_threshold" value="0.25" />
            </section>
            <section name="meta">
                <param name="showcode" value="T"/>
                <param name="warn" value="F"/>
                <param name="varstate" value="F"/>
                <param name="plots" value="feat"/>
            </section>
            <output name="out_html" ftype="html">
                <assert_contents>
                    <has_text text="Seurat Analysis" />
                    <has_text text="Performed using Galaxy" />
                    <has_text text="img src=&quot;data:image/png;base64" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
types of single cell data. See the `Seurat Guided Clustering tutorial`_ for more information.

-----

**Inputs**

    * Gene count matrix in TAB-separated format

-----

**Outputs**

    * HTML of plots

Optionally you can choose to output

    * R commands used to generate plots printed alongside figures

.. _Seurat: https://www.nature.com/articles/nbt.4096
.. _Satija Lab: https://satijalab.org/seurat/
.. _Seurat Guided Clustering tutorial: https://satijalab.org/seurat/pbmc3k_tutorial.html

]]></help>
    <citations>
        <citation type="doi">10.1038/nbt.4096</citation>
    </citations>
</tool>