--- a/scimap_phenotyping.xml	Mon Aug 29 23:55:18 2022 +0000
+++ b/scimap_phenotyping.xml	Mon Jun 10 18:44:25 2024 +0000
@@ -7,19 +7,20 @@
     <expand macro="scimap_requirements"/>
     <expand macro="macro_stdio" />
     <version_command>echo "@VERSION@"</version_command>
-    <command>
+    <command detect_errors="aggressive">
         <![CDATA[
         python '$__tool_directory__/scimap_phenotyping.py'
             --adata '$anndata'
+            #if $log
+                --log
+            #end if
             #if $manual_gates
                 --manual_gates '$manual_gates'
                 --manual_gates_ext '${manual_gates.ext}'
             #end if
             --gating_workflow '$gating_workflow'
             --gating_workflow_ext '${gating_workflow.ext}'
-            #if $rescale_plots
-                --rescale_plots
-            #end if
+            --random_state '$random_state'
             --output '$output'
 
         ]]>
@@ -29,17 +30,14 @@
     </configfiles>
     <inputs>
         <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
+        <param name="log" type="boolean" checked="true" label="Whether to log the data prior to rescaling" />
         <param name="manual_gates" type="data" format="tabular,csv" optional="true" label="Select the dataset containing manual gate information" help="First column as markers and second column as the gate values in log1p scale. If a marker is not included, auto gating
         based on gaussian mixture modeling will be executed. Optional."/>
         <param name="gating_workflow" type="data" format="tabular,csv" label="Select the dataset containing gating workflow" />
-        <param name="rescale_plots" type="boolean" checked="false" label="Save the GMM gates plots If True"/>
+        <param name="random_state" type="integer" value="0" optional="true" label="Set seed used by the random number generator for GMM" />
     </inputs>
     <outputs>
         <data format="h5ad" name="output" />
-	    <collection name="gmm_plots" type="list" label="${tool.name}: GMM-plots"> 
-            <filter>rescale_plots</filter>
-            <discover_datasets pattern="__designation_and_ext__" directory="auto_gating" ext="png"/>
-        </collection>
     </outputs>
     <tests>
         <test>
@@ -63,6 +61,10 @@
 
 AnnData.
 
+**Important Note**
+
+If adata.raw.X exists, it will be used. If adata.raw.X does not exist, adata.X is used 
+
 **Output**
 
 Anndata with "obs/phenotype" added.
@@ -70,6 +72,5 @@
 
         ]]>
     </help>
-    <citations>
-    </citations>
+    <expand macro="citations" />
 </tool>