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+++ b/README	Wed Apr 03 11:20:03 2019 -0400
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+Seurat tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_dim_plot.xml	Wed Apr 03 11:20:03 2019 -0400
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+<tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="2.3.1+galaxy0">
+    <description>graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</description>
+    <macros>
+        <import>seurat_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version" />
+    <command detect_errors="exit_code"><![CDATA[
+        seurat-dim-plot.R
+        --input-object-file '$input'
+        #if $reduction_use
+        --reduction-use '$reduction_use'
+        #end if
+        #if $dim_1
+        --dim-1 $dim_1
+        #end if
+        #if $dim_2
+        --dim-2 $dim_2
+        #end if
+        #if $cells_use
+        --cells-use $cells_use
+        #end if
+        #if $pt_size
+        --pt-size $pt_size
+        #end if
+        #if $label_size
+        --label-size $label_size
+        #end if
+        --do-label $do_label
+        #if $group_by
+        --group-by $group_by
+        #end if
+        #if $plot_title
+        --plot-title '$plot_title'
+        #end if
+        --do-bare $do_bare
+        #if $cols_use
+        --cols-use '$cols_use'
+        #end if
+        #if $pt_shape
+        --pt-shape '$pt_shape'
+        #end if
+        --coord-fixed $coord_fixed
+        --no-axes $no_axes
+        --dark-theme $dark_theme
+        #if $plot_order
+        --plot-order '$plot_order'
+        #end if
+        --png-width $png_width
+        --png-height $png_height
+        --output-image-file $output_image_file
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" format="rdata" label="RDS object" help='File in which a serialized R matrix object may be found'/>
+        <param type="text" name="reduction_use" value='pca' label="Dimensionality reduction" help='Which dimensionality reduction to use. Default is "pca", can also be "tsne", or "ica", assuming these are precomputed' />
+        <param type="integer" name="dim_1" value='1' label="X axis dimension" help='Dimension for x-axis' />
+        <param type="integer" name="dim_2" value='2' label="Y axis dimension" help='Dimension for y-axis' />
+        <param type="data" name="cells_use" format="tabular" label="Cells list" help='File to be used to derive a vector of cells to plot (default is all cells)' optional='true'/>
+        <param type="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting' />
+        <param type="float" name="label_size" value='4' label="Label size" help='Sets size of labels'/>
+        <param type="boolean" name="do_label" checked="false" label='Label clusters' truevalue="TRUE" falsevalue="FALSE" />
+        <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways' />
+        <param type="text" name="plot_title" format="text" label='Plot title' />
+        <param type="boolean" name="do_bare" checked="false" label='Do only minimal formatting' truevalue="TRUE" falsevalue="FALSE" />
+        <param type="text" name="cols_use" format="text" label="Colors" help='Comma-separated list of colors, each color corresponds to an identity class. By default, ggplot assigns colors.' />
+        <param type="text" name="pt_shape" format="text" label="Cell attribute for shape" help='If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells.' />
+        <param type="boolean" name="coord_fixed" checked="false" label="Fixed-scaled coordinate system" help='Use a fixed scale coordinate system (for spatial coordinates). Default is FALSE.' truevalue="TRUE" falsevalue="FALSE" />
+        <param type="boolean" name="no_axes" checked="false" label="Remove Axes" help='Setting to TRUE will remove the axes.' truevalue="TRUE" falsevalue="FALSE" />
+        <param type="boolean" name="dark_theme" checked="false" label='Use a dark theme for the plot..' truevalue="TRUE" falsevalue="FALSE" />
+        <param type="text" name="plot_order" format="text" label="Ident (clusters) order" help='Comma-separated string specifying the order of plotting for the idents (clusters). This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top).' />
+        <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.' />
+        <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
+    </inputs>
+    <outputs>
+        <data name="output_image_file" format="png" from_work_dir="pca.png" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="seurat_clustered.rds" />
+            <output name="output_image_file" file="pca.png" />
+        </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.
+
+This tool graphs the output of a dimensional reduction technique (PCA by default). Cells are colored
+by their identity class.
+
+-----
+
+**Inputs**
+
+    * Seurat RDS object
+
+-----
+
+**Outputs**
+
+    * PNG-format image file
+
+.. _Seurat: https://www.nature.com/articles/nbt.4096
+.. _Satija Lab: https://satijalab.org/seurat/
+
+@VERSION_HISTORY@
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_macros.xml	Wed Apr 03 11:20:03 2019 -0400
@@ -0,0 +1,50 @@
+<?xml version="1.0"?>
+<macros>
+
+    <token name="@VERSION@">0.0.5</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="version">
+    	<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: ")
+    ]]></version_command>
+    </xml>
+
+    <xml name="genes-use-input">
+      <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv, txt" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
+    </xml>
+    <xml name="dims-use-input">
+      <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
+    </xml>
+
+    <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+
+0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9.
+
+2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
+EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(https://github.com/drosofff) and Lea Bellenger(https://github.com/bellenger-l).
+      ]]></token>
+
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/nbt.4096</citation>
+            <citation type="bibtex">
+              @misc{r-seurat-scripts.git,
+              author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
+              year = {2018},
+              title = {Seurat-scripts: command line interface for Seurat},
+              publisher = {GitHub},
+              journal = {GitHub repository},
+              url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
+            }
+            </citation>
+        </citations>
+    </xml>
+</macros>