--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSflowViz.xml	Mon Jun 22 20:48:47 2020 -0400
@@ -0,0 +1,100 @@
+<tool id="flowviz_density_plots" name="Generate stacked density plots" version="1.0+galaxy0">
+  <description>for a set of FCS files</description>
+  <requirements>
+    <requirement type="package" version="1.40.0">bioconductor-flowviz</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" />
+    <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" />
+    <exit_code range="12" level="fatal" description="The set of FCS files must have the same set of channels" />
+  </stdio>
+  <command><![CDATA[
+      Rscript $__tool_directory__/FCSflowViz.R '${channels}' '${output}' '${outformat}'
+      #for $f in $input
+        '${f}' '${f.name}'
+      #end for
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/>
+    <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot all channels."/>
+    <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load.">
+      <option value="PNG">PNG</option>
+      <option value="PDF">PDF</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="png" name="output" label="Stacked Density Plots from ${input.name} in ${outformat}">
+      <change_format>
+        <when input="outformat" value="PDF" format="pdf" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input">
+        <collection type="list">
+          <element name="input1.fcs" value="input1.fcs"/>
+          <element name="input2.fcs" value="input2.fcs"/>
+          <element name="input3.fcs" value="input3.fcs"/>
+        </collection>
+      </param>
+      <param name="channels" value="1,3"/>
+      <param name="outformat" value="PDF"/>
+      <output name="output" file="graph.pdf" compare="sim_size"/>
+    </test>
+    <test>
+      <param name="input">
+        <collection type="list">
+          <element name="input1.fcs" value="input1.fcs"/>
+          <element name="input2.fcs" value="input2.fcs"/>
+          <element name="input3.fcs" value="input3.fcs"/>
+        </collection>
+      </param>
+      <param name="channels" value="i.e.:1,3,4"/>
+      <param name="outformat" value="PNG"/>
+      <output name="output" file="graph.png" compare="sim_size"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+FlowViz stacked 1D density plots
+--------------------------------
+
+This tool generates stacked 1D density plots using flowViz.
+
+**Input files**
+
+This tool takes a collection of valid FCS files as input.
+
+.. class:: warningmark
+
+Each FCS file in the input data collection should have the SAME set of channels.
+
+**Output files**
+
+This tool generates stacked 1D density plots for each channel. A pdf file can optionally be generated.
+
+class:: warningmark
+
+PDF are larger files that may take some time to load. It might be faster to download the PDF output once generated to open it locally.
+
+-----
+
+**Example**
+
+*Output*:
+
+.. image:: ./static/images/flowtools/flowviz.png
+
+-----
+
+**flowViz reference**
+
+Ellis B, Gentleman R, Hahne F, Le Meur N, Sarkar D and Jiang M (2017). flowViz: Visualization for flow cytometry. R package version 1.40.0.
+
+  ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1186/1471-2105-10-106</citation>
+  </citations>
+</tool>