--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat.xml	Sun Aug 26 16:24:02 2018 -0400
@@ -0,0 +1,146 @@
+<tool id="seurat" name="Seurat" version="2.3.4">
+    <description>- toolkit for exploration of single-cell RNA-seq data</description>
+    <requirements>
+        <requirement type="package" version="3.4.1">r-base</requirement>
+        <requirement type="package" version="2.3.4">r-seurat</requirement>
+        <requirement type="package" version="1.0.0">bioconductor-singlecellexperiment</requirement> 
+        <requirement type="package" version="1.6.0">r-optparse</requirement>
+    </requirements>
+    <version_command><![CDATA[
+echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", SingleCellExperiment version" $(R --vanilla --slave -e "library(SingleCellExperiment); cat(sessionInfo()\$otherPkgs\$SingleCellExperiment\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+
+#if $rscript:
+    cp '$__tool_directory__/seurat.R' '$out_rscript' &&
+#end if
+
+Rscript '$__tool_directory__/seurat.R'
+
+--counts '$counts'
+--numPCs $adv.num_PCs
+--min.cells $adv.min_cells
+--min.genes $adv.min_genes
+
+#if $adv.low_thresholds:
+    --low.thresholds $adv.low_thresholds
+#end if
+#if $adv.high_thresholds:
+    --high.thresholds $adv.high_thresholds
+#end if
+#if $adv.x_low_cutoff:
+    --x.low.cutoff $adv.x_low_cutoff
+#end if
+#if $adv.x_high_cutoff:
+    --x.high.cutoff $adv.x_high_cutoff
+#end if
+#if $adv.y_cutoff:
+    --y.cutoff $adv.y_cutoff
+#end if
+#if $adv.cells_use:
+    --cells.use $adv.cells_use
+#end if
+#if $adv.resolution:
+    --resolution $adv.resolution
+#end if
+#if $adv.min_pct:
+    --min.pct $adv.min_pct
+#end if
+#if $adv.logfc_threshold:
+    --logfc.threshold $adv.logfc_threshold
+#end if
+
+#if $rds:
+    --rds '$rds'
+#end if
+
+]]></command>
+
+    <inputs>
+        <param name="counts" type="data" format="tabular" label="Counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/>
+        <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used by this tool will be provided as a text file in the output. Default: No" />
+        <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Seurat RDS object?"
+            help="Output the Seurat RDS object, can be loaded into R. Default: No">
+        </param>
+        <section name="adv" title="Advanced Options">
+            <param argument="--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. Default: 10" />
+            <param argument="--min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells." />
+            <param argument="--min_genes" type="integer" min="0"  value="0" label="Minimum genes" help="Include cells where at least this many genes are detected." />
+            <param argument="--low_thresholds" type="float" optional="True" label="Low threshold for filtering cells" />
+            <param argument="--high_thresholds" type="float" optional="True" label="High threshold for filtering cells" />
+            <param argument="--x_low_cutoff" type="float" optional="True" label="X-axis low cutoff for variable genes" help="Bottom cutoff on x-axis for identifying variable genes" />
+            <param argument="--x_high_cutoff" type="float" optional="True" label="X-axis high cutoff for variable genes" help="Top cutoff on x-axis for identifying variable genes" />
+            <param argument="--y_cutoff" type="float" optional="True" label="Y-axis cutoff for variable genes" help="Bottom cutoff on y-axis for identifying variable genes" />
+            <param argument="--cells_use" type="integer" min="0" optional="True" 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 argument="--resolution" type="float" optional="True" 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 argument="--min_pct" type="float" optional="True" label="Minimum percent cells" help="With FindMarkers only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed. Default is 0.1" />
+            <param argument="--logfc_threshold" type="float" min="0" optional="True" label="LogFC 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. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals." />
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="out_pdf" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots" />
+        <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
+            <filter>rscript</filter>
+        </data>
+        <data name="out_rds" format="rds" from_work_dir="Seurat.rds" label="${tool.name} on ${on_string}: RData file">
+            <filter>rds</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <!-- Ensure count matrix input works -->
+        <test>
+            <param name="counts" ftype="tabular" value="deng_small.tab.gz"/>
+            <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="x_low_cutoff" value="0.0125" />
+            <param name="x_high_cutoff" value="3" />
+            <param name="y_cutoff" value="0.5" />
+            <param name="numPCs" value="10" />
+            <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" />
+            <output name="out_pdf" ftype="pdf" value="out.pdf" compare="sim_size"/>
+        </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**
+
+    * PDF of plots
+
+Optionally you can choose to output
+
+    * Seurat RDS object (can use within R)
+    * Rscript
+
+.. _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>