--- a/raceid_inspectclusters.xml	Mon Apr 15 17:55:46 2019 -0400
+++ b/raceid_inspectclusters.xml	Mon Aug 12 13:01:12 2019 -0400
@@ -1,39 +1,290 @@
-<tool id="raceid_inspectclusters" name="Cluster Inspection using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
+<tool id="raceid_inspectclusters" name="Cluster Inspection using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" >
     <description>examines gene expression within clusters</description>
     <macros>
         <import>macros.xml</import>
-        <import>macros_inspectclusters.xml</import>
+        <import>macros_cheetah.xml</import>
+        <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" >
+            <section name="@SECTIONNAME@" title="@SECTIONTITLE@" expanded="true" >
+                <param name="name_set" type="text" optional="true" label="Name of Set" >
+                    <!-- Aname, Bname -->
+                    <expand macro="sanitize_title" />
+                </param>
+                <conditional name="meth" >
+                    <param name="type" type="select" label="Selection method" >
+                        <option value="cln" selected="true">Cluster Numbers</option>
+                        <option value="regex" >Regular Expression</option>
+                        <option value="manual" >Manual Selection</option>
+                    </param>
+                    <when value="cln" >
+                        <param name="selector" type="text" value="" label="List of clusters" help="Clusters should be listed delimited by commas (e.g. 3,4,5)" >
+                            <expand macro="sanitize_numeric_vector" />
+                        </param>
+                    </when>
+                    <when value="regex" >
+                        <param name="selector" type="text" value="" label="Regular Expression to select gene names" >
+                            <expand macro="sanitize_regex" />
+                        </param>
+                    </when>
+                    <when value="manual" >
+                        <param name="selector" type="text" value="" label="List of genes" >
+                            <expand macro="sanitize_string_vector" />
+                        </param>
+                    </when>
+                </conditional>
+            </section>
+        </macro>
     </macros>
     <expand macro="requirements" />
-    <version_command><![CDATA[
-Rscript '$__tool_directory__/scripts/clusterinspect.R' @GET_VERSION@
-]]></version_command>
-
-    <command detect_errors="exit_code"><![CDATA[
-#set bin = 'clusterinspect.R'
-Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
-    ]]></command>
-  
-    <configfiles>
-        <configfile name="userconf" ><![CDATA[
-@STRING2VECTOR@
-
-@INSPECTCLUSTERS_CHEETAH@
-]]>
-        </configfile>
-    </configfiles>
+    <expand macro="version_command_config" prog="clusterinspect.R" cheetah="INSPECTCLUSTERS_CHEETAH" out="&#38;&#62; '$outlog'" />
     <inputs>
-        <expand macro="inspectclusters_inputs" />
+        <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the cluster analysis" />
+        <conditional name="plotgen">
+            <param name="do_opt" type="select" label="Plot Clusters?" help="Generates tSNE and F-R plots" >
+                <option value="yes" selected="true" >Yes</option>
+                <option value="no" >No</option>
+            </param>
+            <when value="no" />
+            <when value="yes" >
+                <param name="clusts_plot" type="text" label="Cluster Numbers to plot" value="" help="Leave blank to plot all clusters" optional="true" >
+                    <expand macro="sanitize_numeric_vector" />
+                </param>
+            </when>
+        </conditional>
+        <conditional name="plotsym" >
+            <param name="do_opt" type="select" label="Perform Subset Analysis?" >
+                <expand macro="yesno_checkedno" />
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="types_regex" type="text" optional="true" label="Types Regex (removal)" help="Regular expression to be used to remove portions of the cell names, in order to indicate cell type. e.g. if your cells are labelled as 'cdk5_1, cdk5_2, glow_1, glow_2', then a regex of '_\\d$' would trim off the ends and set the cell types to 'cdk5, cdk5, glow, glow'. " >
+                    <expand macro="sanitize_regex" />
+                </param>
+                <expand macro="use_defaults_no" >
+                    <param name="subset_regex" type="text" optional="true" label="Subset of Types: Regex (select)" help="Regular expression to be used to select for cell types of interest. e.g. if we are only interested in 'cdk5' positive cells, then we would simply put 'cdk5' here. ">
+                        <expand macro="sanitize_regex" />
+                    </param>
+                    <param name="fr" type="boolean" checked="false" label="Output FR map instead of tSNE" help="Performs a Fruchterman-Rheingold projection instead of tSNE" />
+                </expand>
+            </when>
+        </conditional>
+        <conditional name="gois" >
+            <param name="do_opt" type="select" label="Examine Genes of Interest" >
+                <expand macro="yesno_checkedno" />
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="inspect_goi_genes" type="text" value="" label="Genes to Examine" >
+                    <expand macro="sanitize_string_vector" />
+                </param>
+                <param name="inspect_goi_cells" type="text" optional="true" label="Cells to Examine" help="Leave blank to examine all" ><!-- "":NULL -->
+                    <expand macro="sanitize_string_vector" />
+                </param>
+                <expand macro="use_defaults_no" >
+                    <!-- Yes, examine genes of interest, but no do not use defaults... -->
+                    <param name="inspect_goi_imputed" type="boolean" checked="false" label="Impute Genes" help="Only works if k-nearest neighbours was used in the clustering" />
+                    <param name="plotexp_n" type="text" optional="true" label="Title of plot" help="If blank, the list of genes are used" >
+                        <expand macro="sanitize_title" />
+                    </param>
+                    <param name="plotmarkg_cthr" type="integer" min="0" value="0" label="Cluster Threshold" help="Include only clusters with cells greater than this" />
+                    <param name="plotmarkg_cl" type="text" optional="true" label="Cluster List" help="List of cluster numbers to include. Leave blank to include all" >
+                        <expand macro="sanitize_numeric_vector" />
+                    </param><!-- "":NULL -->
+                    <param name="plotmarkg_order_cells" type="boolean" checked="false" label="Order Cells" help="Order heatmap by cell names, not by cluster" />
+                    <param name="plotmarkg_aggr" type="boolean" checked="false" label="Average Expression" help="Show only average expression for each cluster" />
+                    <param name="plotmarkg_norm" type="boolean" checked="false" label="Normalise Gene Expression " help="Normalise gene expression to 1 to depict genes on the same scale" />
+                    <param name="plotmarkg_flo" type="integer" max="-5" optional="true" label="Lower-bound for Gene Expression" /><!-- negative or null vals only for this seem to work-->
+                    <param name="plotmarkg_cap" type="integer" min="1" optional="true" label="Upper-bound for Gene Expression" />
+                    <param name="plotmarkg_samples" type="text" optional="true" label="Regex to Select Sample Names For Each cell" >
+                        <expand macro="sanitize_regex" />
+                    </param>
+                    <param name="plotmarkg_cluster_cols" type="boolean" checked="false" label="Cluster columns" />
+                    <param name="plotmarkg_cluster_rows" type="boolean" checked="true" label="Cluster rows" />
+                    <param name="plotmarkg_cluster_set" type="boolean" checked="false" label="Order Clusters by Heirarchal Clustering of Cluster Medoids." />
+                </expand>
+            </when>
+        </conditional>
+        <conditional name="diffgtest" >
+            <param name="do_opt" type="select" label="Differential Gene Testing" >
+                <expand macro="yesno_checkedno" />
+            </param>
+            <when value="no" />
+            <when value="yes" >
+                <expand macro="select_cells" sectionname="set_a" sectiontitle="Cells in Set A" />
+                <expand macro="select_cells" sectionname="set_b" sectiontitle="Cells in Set B" />
+                <expand macro="use_defaults_no" >
+                    <param name="plotdiffg_pthr" type="float" min="0" max="1" value="0.05" label="P-value cutoff" help="Cutoff for displaying differentially expressed genes" />
+                    <param name="plotdiffg_padj" type="boolean" checked="true" label="Apply B-H Correction" help="Display genes with a Benjamini-Hochberg corrected false discovery rate lower than the above P-value threshold" />
+                    <param name="plotdiffg_lthr" type="float" min="0" value="0" label="Log2-Fold Threshold" help="Differentially expressed genes are displayed only for log2 fold-changes higher than this" />
+                    <param name="plotdiffg_mthr" type="float" optional="true" label="Log2 Mean Threshold" help="Differentially expressed genes are displayed only for log2 mean expression greater than this" /><!-- opt:-Inf -->
+                    <param name="plotdiffg_show_names" type="boolean" checked="false" label="Display Gene Names" />
+                </expand>
+            </when>
+        </conditional>
     </inputs>
-
     <outputs>
         <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
-        <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
-            <filter>use_log</filter>
-        </data>
+        <data name="outlog" format="txt" hidden="true"  /><!-- useful for debugging, but hide from user -->
     </outputs>
     <tests>
-        <expand macro="inspectclusters_tests" />
+        <test><!-- general plots, plotgen -->
+            <param name="inputrds" value="out_cluster_default.rdat" />
+            <conditional name="plotgen" >
+                <param name="do_opt" value="yes" />
+            </conditional>
+            <output name="outpdf" value="out_cluster_general_default.pdf" lines_diff="30" />
+        </test>
+        <test><!-- general plots, plotgen with cluster 1,8,5 only -->
+            <param name="inputrds" value="out_cluster_default.rdat" />
+            <conditional name="plotgen" >
+                <param name="do_opt" value="yes" />
+                <param name="clusts_plot" value="1,8,5" />
+            </conditional>
+            <output name="outpdf" value="out_cluster_general_default.pdf" lines_diff="30" />
+        </test>
+        <test><!-- default test, plotsym -->
+            <param name="inputrds" value="out_cluster_default.rdat" />
+            <conditional name="plotsym" >
+                <param name="do_opt" value="yes" />
+                <param name="types_regex" value="\\_\\d+" />
+                <expand macro="test_nondef" >
+                    <param name="subset_regex" value="IV|V" />
+                </expand>
+            </conditional>
+            <conditional name="gois" >
+                <param name="do_opt" value="yes" />
+                <param name="inspect_goi_genes" value="Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5" />
+            </conditional>
+            <output name="outpdf" value="out_cluster_inspect_default.pdf" lines_diff="30" />
+        </test>
+        <test><!-- Advanced 1 -->
+            <param name="inputrds" value="out_cluster_default.rdat" />
+            <conditional name="plotsym" >
+                <param name="do_opt" value="yes" />
+                <param name="types_regex" value="\\_\\d+" />
+                <expand macro="test_nondef" >
+                    <param name="subset_regex" value="IV|V" />
+                    <param name="fr" value="true" />
+                </expand>
+            </conditional>
+            <conditional name="gois" >
+                <param name="do_opt" value="yes" />
+                <param name="inspect_goi_genes" value="Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5" />
+                <expand macro="test_nondef" >
+                    <param name="inspect_goi_imputed" value="false" />
+                    <param name="plotexp_n" value="Test Title" />
+                    <param name="plotmarkg_order_cells" value="true" />
+                    <param name="plotmarkg_aggr" value="true" />
+                    <param name="plotmarkg_norm" value="true" />
+                    <param name="plotmarkg_flo" value="-10" />
+                    <param name="plotmarkg_cap" value="100" />
+                    <param name="plotmarkg_samples" value="(\\_\\d+)$" />
+                    <param name="plotmarkg_cluster_cols" value="true" />
+                    <param name="plotmarkg_cluster_rows" value="false" />
+                    <param name="plotmarkg_cluster_set" value="true" />
+                </expand>
+            </conditional>
+            <conditional name="diffgtest" >
+                <param name="do_opt" value="yes" />
+                <section name="set_a" >
+                    <param name="name_set" value="Test set A" />
+                    <conditional name="meth" >
+                        <param name="type" value="regex" />
+                        <param name="selector" value="^V5.*" />
+                    </conditional>
+                </section>
+                <section name="set_b" >
+                    <param name="name_set" value="Test set B" />
+                    <conditional name="meth" >
+                        <param name="type" value="manual" />
+                        <param name="selector" value="I5d_3,I5d_4,I5d_6,I5d_8,I5d_9,I5d_10,I5d_11,I5d_12,I5d_13,I5d_14" />
+                    </conditional>
+                </section>
+                <expand macro="test_nondef" >
+                    <param name="plotdiffg_pthr" value="0.1" />
+                    <param name="plotdiffg_padj" value="false" />
+                    <param name="plotdiffg_lthr" value="0.2" />
+                    <param name="plotdiffg_mthr" value="0.2" />
+                    <param name="plotdiffg_show_names" value="true" />
+                </expand>
+            </conditional>
+            <output name="outpdf" value="out_cluster_inspect_advanced1.pdf" lines_diff="30"/>
+        </test>
+        <test><!-- Advanced 2 -->
+            <param name="inputrds" value="out_cluster_default.rdat" />
+            <conditional name="plotsym" >
+                <param name="do_opt" value="yes" />
+                <expand macro="test_nondef" >
+                    <param name="fr" value="false" />
+                </expand>
+            </conditional>
+            <conditional name="gois" >
+                <param name="do_opt" value="yes" />
+                <param name="inspect_goi_genes" value="Sp1,Spc24,Spcs1,Spcs2,Spcs3" />
+                <expand macro="test_nondef" >
+                    <param name="plotexp_n" value="Test Title 2" />
+                    <param name="plotmarkg_order_cells" value="true" />
+                    <param name="plotmarkg_aggr" value="true" />
+                    <param name="plotmarkg_norm" value="false" />
+                    <param name="plotmarkg_flo" value="-10" />
+                    <param name="plotmarkg_cap" value="10" />
+                    <param name="plotmarkg_cluster_cols" value="true" />
+                    <param name="plotmarkg_cluster_rows" value="true" />
+                    <param name="plotmarkg_cluster_set" value="true" />
+                </expand>
+            </conditional>
+            <conditional name="diffgtest" >
+                <param name="do_opt" value="yes" />
+                <section name="set_a" >
+                    <param name="name_set" value="Test set A" />
+                    <conditional name="meth" >
+                        <param name="type" value="regex" />
+                        <param name="selector" value="^IV.*" />
+                    </conditional>
+                </section>
+                <section name="set_b" >
+                    <param name="name_set" value="Test set B" />
+                    <conditional name="meth" >
+                        <param name="type" value="cln" />
+                        <param name="selector" value="3" />
+                    </conditional>
+                </section>
+                <expand macro="test_nondef" >
+                    <param name="plotdiffg_pthr" value="0.8" />
+                    <param name="plotdiffg_padj" value="true" />
+                    <param name="plotdiffg_lthr" value="0.8" />
+                    <param name="plotdiffg_mthr" value="0.8" />
+                    <param name="plotdiffg_show_names" value="false" />
+                </expand>
+            </conditional>
+            <output name="outpdf" value="out_cluster_inspect_advanced2.pdf" lines_diff="30"/>
+        </test>
+        <test><!-- Advanced 3 -->
+            <param name="inputrds" value="out_cluster_default.rdat" />
+            <conditional name="plotsym" >
+                <param name="do_opt" value="no" />
+            </conditional>
+            <conditional name="gois" >
+                <param name="do_opt" value="no" />
+            </conditional>
+            <conditional name="diffgtest" >
+                <param name="do_opt" value="yes" />
+                <section name="set_a" >
+                    <param name="name_set" value="Test set A" />
+                    <conditional name="meth" >
+                        <param name="type" value="cln" />
+                        <param name="selector" value="1,2" />
+                    </conditional>
+                </section>
+                <section name="set_b" >
+                    <param name="name_set" value="Test set B" />
+                    <conditional name="meth" >
+                        <param name="type" value="cln" />
+                        <param name="selector" value="3,4,6" />
+                    </conditional>
+                </section>
+            </conditional>
+            <output name="outpdf" value="out_diffgene_multiple.pdf" lines_diff="30"/>
+        </test>
     </tests>
     <help><![CDATA[
 
@@ -50,12 +301,12 @@
    * Produces a tSNE of all clusters, as well as a force-directed Fruchterman-Reingold (F-R) layout which may have tidier plots.
  * Perform Subset Analysis:
    * tSNE and F-R plots with cells whose name match the specified regex highlighted
-   
+
  * Examine Genes of Interest:
    * Expression plots highlighting a gene or genes of interest across all clusters
 
- * Differential Gene Testing: 
-   * Examining the expression between 
+ * Differential Gene Testing:
+   * Examining the expression between
 
  * A list of the most differentially expressed genes in each cluster
  * An output PDF that provides heatmaps for: