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+++ b/README	Wed Apr 03 11:17:29 2019 -0400
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+Seurat tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_find_markers.xml	Wed Apr 03 11:17:29 2019 -0400
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+<tool id="seurat_find_markers" name="Seurat FindMarkers" version="2.3.1+galaxy1">
+    <description>find markers (differentially expressed genes)</description>
+    <macros>
+        <import>seurat_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version" />
+    <command detect_errors="exit_code"><![CDATA[
+seurat-find-markers.R
+
+--input-object-file '$input'
+--output-text-file output.txt
+
+#if $genes_use:
+  --genes-use '$genes_use'
+#end if
+
+#if str($logfc_threshold):
+  --logfc-threshold '$logfc_threshold'
+#end if
+
+#if str($adv.min_pct):
+  --min-pct '$adv.min_pct'
+#end if
+
+#if str($adv.min_diff_pct):
+  --min-diff-pct '$adv.min_diff_pct'
+#end if
+
+#if $adv.only_pos:
+  --only-pos '$adv.only_pos'
+#end if
+
+--test-use '$adv.test_use'
+
+#if str($max_cells_per_ident):
+  --max-cells-per-ident '$max_cells_per_ident'
+#end if
+
+#if str($min_cells_per_gene):
+  --min-cells-gene '$min_cells_per_gene'
+#end if
+
+#if str($min_cells_group):
+  --min-cells-group '$min_cells_group'
+#end if
+
+
+]]></command>
+
+    <inputs>
+        <param name="input" type="data" format="rdata" label="RDS object" />
+        <expand macro="genes-use-input"/>
+        <param name="logfc_threshold" label="LogFC logfc_threshold" optional="true" argument="--logfc-threshold" type="float" help="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."/>
+        <param name="max_cells_per_ident" label="Max cells per ident" optional="true" argument="--max-cells-per-ident" type="integer" help="Down sample each identity class to a max number. Default is no downsampling. Not activated by default (set to Inf)."/>
+        <param name="min_cells_per_gene" label="Min cells per gene" optional="true" argument="--min-cells-gene" type="integer" help="Minimum number of cells expressing the gene in at least one of the two groups, currently only used for poisson and negative binomial tests."/>
+        <param name="min_cells_group" label="Min cells in one of the groups" optional="true" argument="--min-cells-group" type="integer"/>
+        <section name="adv" title="Advanced Options">
+            <param name="min_pct" type="float" label="Min Pct" optional="true" help="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 name="min_diff_pct" type="float" label="Min diff Pct" optional="true" help="Only test genes that show a minimum difference in the fraction of detection between the two groups. Set to -Inf by default."/>
+            <param name="only_pos" type="boolean" label="Only positive markers" truevalue="TRUE" falsevalue="" help="Only return positive markers (FALSE by default)."/>
+            <param name="test_use" type="select" label="Test to use" help="">
+              <option value="wilcox" selected="true">Wilcoxon</option>
+              <option value="bimod">Bi-modal</option>
+              <option value="roc">ROC</option>
+              <option value="t">t-Test</option>
+              <option value="tobit">tobit</option>
+              <option value="poisson">Poisson</option>
+              <option value="negbinom">Negative binomia</option>
+              <option value="MAST">MAST</option>
+              <option value="DESeq2">DESeq2</option>
+            </param>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="txt" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Text file"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" ftype="rdata" value="out_runtsne.rds"/>
+            <output name="output" ftype="txt" value="out_findmark.txt"/>
+        </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 finds markers (differentially expressed genes) for each of the identity classes in a dataset. It outputs a text file containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)
+
+-----
+
+**Inputs**
+
+    * RDS object
+
+-----
+
+**Outputs**
+
+    * Text 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 11:17:29 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>