--- a/scpred_get_feature_space.xml	Fri Aug 14 11:15:15 2020 -0400
+++ b/scpred_get_feature_space.xml	Fri Nov 27 13:45:33 2020 +0000
@@ -5,28 +5,34 @@
     </macros>
     <expand macro='requirements' />
     <command detect_errors='exit_code'><![CDATA[
-        scpred_get_feature_space.R  --input-object '${input_object}'  --prediction-column '${prediction_column}'  --output-path '${output_obj_path}' 
+        scpred_get_feature_space.R  --input-object '${input_object}'  --prediction-column '${prediction_column}'   --output-path '${output_obj_path}' 
+     
+        #if $correction_method
+        --correction-method '${correction_method}' 
+        #end if
+        #if $significance_threshold
+        --significance-threshold '${significance_threshold}'
+        #end if 
+        #if $reduction_parameter
+        --reduction-parameter '${reduction_parameter}'
+        #end if 
 
-        #if $explained_var_limit
-        --explained-var-limit '${explained_var_limit}'
-        #end if
-        #if $eigenvalue_plot_path
-        --eigenvalue-plot-path '${eigenvalue_plot_path}'
-        #end if
+
         ]]></command>
     <inputs>
-        <param type='data' name='input_object' label='Input SCE object' format='rdata' help='Input SCE object in .rds format' />
-        <param type='text' name='prediction_column' label='Prediction column' help='Name of the metadata column that contains training labels' />
-        <param type='float' name='explained_var_limit' label='Limit of explained variance' value="0.01" help='Threshold to filter principal components based on variance explained' />
+        <param type='data' name='input_object' label='Input Seurat object' format='rdata' help='Input Seurat object in .rds format' />
+        <param type='text' name='prediction_column' optional="true" value="cell_type" label='Prediction Column' help='Name of the metadata column that contains training labels' />
+        <param type='text' name='correction_method' label='Correction Method' optional='true' value="fdr" help='Method for mulpiple testing correction' />
+        <param type='float' name='significance_threshold' label='Significance Threshold' optional='true' value="1.0" help='Significance threshold for principal components explaining class identity' />
+        <param type='text' name='reduction_parameter' label='Reduction Parameter' optional='true' value="pca" help='Name of reduction in Seurat objet to be used to determine the feature space. Default: "pca"' />
+        
     </inputs>
     <outputs>
         <data name='output_obj_path' format='rdata' />
-        <data name='eigenvalue_plot_path' format='png' />
     </outputs>
      <tests>
         <test>
-            <param name="input_object" value="scPred_object.rds" />
-            <param name="prediction_column" value="cell_type2" />
+            <param name="input_object" value="reference_pbmc.rds" />
             <output name="output_obj_path" file="scPred_feat_space.rds" compare="sim_size" />
         </test>
     </tests>