--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FlowSOMGenerateTree.xml	Tue Jun 23 12:46:08 2020 -0400
@@ -0,0 +1,229 @@
+<tool id="flowsom_tree" name="Generate a reference Self Organizing Map" version="1.0+galaxy1">
+  <description>using FlowSOM.</description>
+  <requirements>
+    <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="10" level="fatal" description="Please provide a valid input (FCS or flowFrame)." />
+    <exit_code range="11" level="fatal" description="Please provide integers for columns you want to analyze, in a comma separated list." />
+    <exit_code range="12" level="fatal" description="Provided indices are out of range in the FCS file / flowframe given as input." />
+    <exit_code range="13" level="fatal" description="Please provide integers for the number of expected clusters." />
+    <exit_code range="14" level="fatal" description="Please provide integers for the grid size." />
+    <exit_code range="15" level="fatal" description="Please provide an integer to set the seed." />
+  </stdio>
+  <command><![CDATA[
+      Rscript $__tool_directory__/FlowSOMGenerateTree.R '${input}' '${output}' '${cols}' '${cluster}' '${xdim}' '${ydim}' '${seed}'
+      #if $plotoutput.plot == "TRUE"
+        '${treeplot}' '${plotoutput.plotformat}' '${plotoutput.nodesize}'
+      #end if
+      #if $mplot == "TRUE"
+        '${mrkrplot}'
+      #end if
+      #if $txtoutput.table == "TRUE"
+        '${txtoutput.tablecontent}' '${txttable}' '${mappingtable}' 'mm' 'mm'
+      #end if
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs, flowframe" name="input" type="data" label="FCS file or flowFrame" />
+    <param name="cols" type="text" value="i.e.:1,2,5" label="Columns to use for analysis" help="By default, all markers except for FSC and SSC will be taken into account." />
+    <param name="cluster" type="integer" value="10" optional="true" label="Number of expected metaclusters" help="By default, the number of expected metaclusters is set to 10" />
+    <param name="xdim" type="integer" value="10" label="Grid size, width"/>
+    <param name="ydim" type="integer" value="10" label="Grid size, height"  help="By default, the grid size is 10x10. The grid size specifies the number of clusters." />
+    <param name="seed" type="integer" value="42" label="Seed"  help="Let's be geeks, default is set to 42." />
+    <conditional name="txtoutput">
+      <param name="table" type="boolean" label="Output text?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
+      <when value="TRUE">
+        <param name="tablecontent" type="select" label="Associate each event to SOM clusters or meta-clusters?">
+          <option value="FlowSOM">FlowSOM Clusters</option>
+          <option value="meta">Meta-Clusters</option>
+        </param>
+      </when>
+    </conditional>
+    <conditional name="plotoutput">
+      <param name="plot" type="boolean" label="Plot SOM Tree?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
+      <when value="TRUE">
+        <param name="nodesize" type="boolean" label="Make all nodes the same size?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
+        <param name="plotformat" type="select" label="Graph output Format">
+          <option value="PNG">PNG</option>
+          <option value="PDF">PDF</option>
+        </param>
+      </when>
+    </conditional>
+    <param name="mplot" type="boolean" label="Plot individual marker trees?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
+  </inputs>
+  <outputs>
+    <data format="fsom" name="output" label="FlowSOM tree from ${input.name}">
+    </data>
+    <data format="flowclr" name="txttable" label="FlowSOM tree on ${input.name} with ${txtoutput.tablecontent} clusters">
+      <filter>txtoutput['table']</filter>
+    </data>
+    <data format="tabular" name="mappingtable" label="Mapping of nodes to meta-clusters from FlowSOM tree on ${input.name}">
+      <filter>txtoutput['table']</filter>
+    </data>
+    <data format="png" name="treeplot" label="Representation of FlowSOM tree on ${input.name} in ${plotoutput.plotformat}">
+      <filter>plotoutput['plot']</filter>
+      <change_format>
+        <when input="plotoutput.plotformat" value="PDF" format="pdf" />
+      </change_format>
+    </data>
+    <data format="pdf" name="mrkrplot" label="Marker trees from FlowSOM on ${input.name}">
+      <filter>(mplot)</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input.fcs"/>
+      <param name="cols" value="3,4,5"/>
+      <param name="cluster" value="10"/>
+      <param name="xdim" value="10"/>
+      <param name="ydim" value="10"/>
+      <param name="seed" value="33"/>
+      <param name="plot" value="FALSE"/>
+      <param name="table" value="FALSE" />
+      <param name="mplot" value="FALSE"/>
+      <output name="output" file="output1.fsom" compare="sim_size"/>
+    </test>
+    <test>
+      <param name="input" value="input.flowframe"/>
+      <param name="cols" value="3,4,5"/>
+      <param name="cluster" value="15"/>
+      <param name="xdim" value="10"/>
+      <param name="ydim" value="10"/>
+      <param name="seed" value="33"/>
+      <param name="plot" value="TRUE"/>
+      <param name="nodesize" value="FALSE"/>
+      <param name="mplot" value="FALSE"/>
+      <param name="plotformat" value="PNG"/>
+      <param name="table" value="FALSE" />
+      <output name="output" file="output2.fsom" compare="sim_size"/>
+      <output name="treeplot" file="tree.png" compare="sim_size"/>
+    </test>
+    <test>
+      <param name="input" value="input.fcs"/>
+      <param name="cols" value="3,4,5"/>
+      <param name="cluster" value="15"/>
+      <param name="xdim" value="10"/>
+      <param name="ydim" value="10"/>
+      <param name="seed" value="33"/>
+      <param name="plot" value="TRUE"/>
+      <param name="nodesize" value="FALSE"/>
+      <param name="mplot" value="TRUE"/>
+      <param name="plotformat" value="PDF"/>
+      <param name="table" value="FALSE" />
+      <output name="output" file="output3.fsom" compare="sim_size"/>
+      <output name="treeplot" file="tree.pdf" compare="sim_size" delta="100000"/>
+      <output name="mrkrplot" file="mrkrplot.pdf" compare="sim_size" delta="100000"/>
+    </test>
+    <test>
+      <param name="input" value="input.fcs"/>
+      <param name="cols" value="3,4,5"/>
+      <param name="cluster" value="10"/>
+      <param name="xdim" value="7"/>
+      <param name="ydim" value="7"/>
+      <param name="seed" value="33"/>
+      <param name="plot" value="FALSE"/>
+      <param name="mplot" value="FALSE"/>
+      <param name="table" value="TRUE" />
+      <param name="tablecontent" value="FlowSOM" />
+      <output name="output" file="output4.fsom" compare="sim_size"/>
+      <output name="txttable" file="output5.flowclr" compare="sim_size"/>
+      <output name="mappingtable" file="mapping1.tabular" compare="sim_size"/>
+    </test>
+    <test>
+      <param name="input" value="input.fcs"/>
+      <param name="cols" value="3,4,5"/>
+      <param name="cluster" value="10"/>
+      <param name="xdim" value="7"/>
+      <param name="ydim" value="7"/>
+      <param name="seed" value="33"/>
+      <param name="plot" value="FALSE"/>
+      <param name="mplot" value="FALSE"/>
+      <param name="table" value="TRUE" />
+      <param name="tablecontent" value="meta" />
+      <output name="output" file="output6.fsom" compare="sim_size"/>
+      <output name="txttable" file="output7.flowclr" compare="sim_size"/>
+      <output name="mappingtable" file="mapping2.tabular" compare="sim_size"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+Generate reference SOM
+-----
+
+This tool generates a reference Self-Organizing Map using FlowSOM.
+
+**Input files**
+
+This tool require a valid FCS file or flowFrame as input.
+
+.. class:: warningmark
+
+Compensation and Transformation will NOT be applied with this tool.
+
+**Parameters**
+
+*Columns to use*
+
+Please indicate the indices of the markers to use in the computation of the SOM in a comma-separated list.
+
+.. class:: infomark
+
+Tip: One of the tools in the FCS File Tools section can help check the markers and channels indices:
+
+- Get list of markers and channels in FCS files.
+
+*Number of meta-clusters*
+
+Please indicate the exact number of meta-clusters expected.
+
+*Grid dimension*
+
+Please indicate the dimension of the grid for establishing the SOM. The dimension of the grid defines the number of clusters (height x width = cluster)
+
+*Seed*
+
+Please indicate a random number to use as seed. To make your analysis reproducible, use the same seed.
+
+**Output files**
+
+This tool produces a FlowSOM object and optionally two sets of plots, one representing the SOM Tree generated, and the other displaying each marker's contribution to the tree. A flat text file can also optionally be generated and used as input for vizualisation tools.
+
+.. 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 text file*::
+
+   Marker1 Marker2 Marker3 ... Population
+   34      45      12      ... 1
+   33      65      10      ... 5
+   19      62      98      ... 2
+   12      36      58      ... 1
+   ...     ...     ...     ... ...
+
+*Node/Meta-cluster mapping file*::
+
+   Node Meta-Cluster
+   1    10
+   2    9
+   3    1
+   4    9
+   ...  ...
+
+*FlowSOM tree*:
+
+.. image :: .static/images/flowtools/FlowSOM_tree.png
+
+*Marker plots*:
+
+.. image:: .static/images/flowtools/flowSOM_marker.png
+  ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1002/cyto.a.22625</citation>
+  </citations>
+</tool>