--- a/raceid_trajectory.xml	Mon Apr 15 17:50:32 2019 -0400
+++ b/raceid_trajectory.xml	Mon Aug 12 12:57:37 2019 -0400
@@ -1,29 +1,45 @@
-<tool id="raceid_trajectory" name="Lineage computation using StemID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
+<tool id="raceid_trajectory" name="Lineage computation using StemID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" >
     <description>generates lineage from prior clustering</description>
     <macros>
         <import>macros.xml</import>
-        <import>macros_trajectory.xml</import>
+        <import>macros_cheetah.xml</import>
     </macros>
     <expand macro="requirements" />
-    <version_command><![CDATA[
-Rscript '$__tool_directory__/scripts/pseudotemporal.R' @GET_VERSION@
-]]></version_command>
+    <expand macro="version_command_config" prog="pseudotemporal.R" cheetah="TRAJECTORY_CHEETAH" />
 
-    <command detect_errors="exit_code"><![CDATA[
-#set bin = 'pseudotemporal.R'
-Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
-    ]]></command>
-  
-    <configfiles>
-        <configfile name="userconf" ><![CDATA[
-@STRING2VECTOR@
-
-@TRAJECTORY_CHEETAH@
-]]>
-        </configfile>
-    </configfiles>
     <inputs>
-        <expand macro="trajectory_inputs" />
+        <param name="inputrds" type="data" format="rdata" label="Input RDS" help="This is the output RData file given by the Cluster stage" />
+        <section name="projcell" title="Compute transcriptome entropy of each cell" expanded="true" >
+            <param name="knn" type="integer" min="0" value="3" label="KNN" help="Number of nearest neighbours to consider." />
+            <param name="cthr" type="integer" min="0" value="5" label="Cluster Threshold" help="Clusters to be included in the StemID analysis must have more than this number of cells" />
+            <expand macro="use_defaults_no" >
+                <param name="nmode" type="boolean" checked="true" label="Neighbour Mode" help="Assign a cell of a given cluster to the cluster with the smallest average distance of the knn nearest neighbours within this cluster." />
+                <param name="fr" type="boolean" checked="false" label="F-R layout?" help="Use Fruchterman-Rheigold layout instead of t-SNE" />
+            </expand>
+        </section>
+        <section name="projback" title="Compute Cell Projections for Randomized Background Distribution" expanded="true" >
+            <param name="pdishuf" type="integer" min="100" value="2000" label="Shuffle Projections" help="Number of randomizations of cell positions for which to compute projections of cells on inter-cluster links" />
+            <expand macro="use_defaults_no" >
+                <param name="fast" type="boolean" checked="false" label="Use a fast approximate background model to infer links" />
+                <param name="rseed" type="integer" value="17000" label="Random seed" />
+            </expand>
+        </section>
+        <section name="comppval" title="Computing P-values for Link Significance" expanded="true" >
+            <param name="pthr" type="float" value="0.01" label="P-value cutoff" help="Cutoff for link significance. This threshold is applied for the calculation of link scores reflecting how uniformly a link is occupied by cells." />
+            <param name="sensitive" type="boolean" checked="false" label="Sensitivity" help="All cells on the most highly significant link are and the link itself are disregard to test significance of the remaining links with a binomial p-value" />
+        </section>
+        <section name="plotgraph" title="StemID2 Lineage Graph" expanded="true" >
+            <param name="showcells" type="boolean" checked="false" label="Show Cells" help="Projections of cells are shown in the plot" />
+            <param name="scthr" type="float" min="0" max="1" value="0" label="Score Threshold" help="Score threshold for links to be shown in the graph" />
+            <expand macro="use_defaults_no">
+                <param name="showtsne" type="boolean" checked="true" label="Show tSNE" help="Show transparent t-SNE map of cells in the background" />
+                <param name="tp" type="float" min="0" max="1" value="0.5" label="Transparency" help="Level of transparency of t-SNE map" />
+            </expand>
+        </section>
+        <section name="compscore" title="Compute StemID2 score" expanded="true" >
+            <param name="nn" type="integer" min="0" value="1" label="Number of Neighbours" help="Number of higher order neighbours to be included for the determination of links" />
+            <param name="scthr" type="float" min="0" max="1" value="0" label="Score Threshold" help="Score threshold for links to be included in the calculation" />
+        </section>
         <param name="use_log" type="boolean" checked="false" label="Output Log?" />
     </inputs>
     <outputs>
@@ -34,7 +50,85 @@
         </data>
     </outputs>
     <tests>
-        <expand macro="trajectory_tests" />
+        <test>
+            <!-- All defaults -->
+            <param name="inputrds" value="out_cluster_default.rdat" />
+            <output name="outpdf" value="out_traject_default.pdf" compare="sim_size" delta="15" />
+            <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="15" />
+        </test>
+        <test>
+            <!-- Manually specify the defaults: should ideally give same output as above test -->
+            <param name="inputrds" value="out_cluster_default.rdat" />
+            <section name="projcell" >
+                <param name="knn" value="3" />
+                <param name="cthr" value="5" />
+                <expand macro="test_nondef" >
+                    <param name="nmode" value="true" />
+                    <param name="fr" value="false" />
+                </expand>
+            </section>
+            <section name="projback" >
+                <param name="pdishuf" value="2000" />
+                <expand macro="test_nondef" >
+                    <param name="fast" value="false" />
+                    <param name="rseed" value="17000" />
+                </expand>
+            </section>
+            <section name="comppval" >
+                <param name="pthr" value="0.01" />
+                <param name="sensitive" value="false" />
+            </section>
+            <section name="plotgraph" >
+                <param name="showcells" value="false" />
+                <param name="scthr" value="0" />
+                <expand macro="test_nondef" >
+                    <param name="showtsne" value="true" />
+                    <param name="tp" value="0.5" />
+                </expand>
+            </section>
+            <section name="compscore" >
+                <param name="nn" value="1" />
+                <param name="scthr" value="0" />
+            </section>
+            <output name="outpdf" value="out_traject_default.pdf" compare="sim_size" delta="15" />
+            <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="15" />
+        </test>
+        <test>
+            <!-- Non-defaults -->
+            <param name="inputrds" value="out_cluster_default.rdat" />
+            <section name="projcell">
+                <param name="knn" value="4" />
+                <param name="cthr" value="4" />
+                <expand macro="test_nondef" >
+                    <param name="nmode" value="false" />
+                    <param name="fr" value="true" />
+                </expand>
+            </section>
+            <section name="projback">
+                <param name="pdishuf" value="1500" />
+                <expand macro="test_nondef" >
+                    <param name="fast" value="true" />
+                    <param name="rseed" value="1500" />
+                </expand>
+            </section>
+            <section name="comppval">
+                <param name="pthr" value="0.05" />
+                <param name="sensitive" value="true" />
+            </section>
+            <section name="plotgraph">
+                <param name="showcells" value="true" />
+                <param name="scthr" value="0.5" />
+                <expand macro="test_nondef" >
+                    <param name="showtsne" value="false" />
+                    <param name="tp" value="0.25" />
+                </expand>
+            </section>
+            <section name="compscore">
+                <param name="nn" value="2" />
+                <param name="scthr" value="0.5" />
+            </section>
+            <output name="outpdf" value="out_traject_adv_nondef.pdf" compare="sim_size" delta="15" />
+        </test>
     </tests>
     <help><![CDATA[
 StemID2