# HG changeset patch
# User ebi-gxa
# Date 1588178544 14400
# Node ID 051f5801c81979befec2be9e7272b06374dcfdb0
# Parent  f0862eb4f99969d168318d32d0a5052ead75571e
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"

diff -r f0862eb4f999 -r 051f5801c819 scpred_predict.xml
--- a/scpred_predict.xml	Fri Apr 24 11:26:54 2020 -0400
+++ b/scpred_predict.xml	Wed Apr 29 12:42:24 2020 -0400
@@ -1,11 +1,25 @@
-<tool id="scpred_predict_labels" name="Scpred predict" version="@TOOL_VERSION@+galaxy0">
+<tool id="scpred_predict_labels" name="Scpred predict" version="@TOOL_VERSION@+galaxy1">
     <description>Make cell type predictions using trained model.</description>
      <macros>
         <import>scpred_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scpred_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --test-labels "${test_labels}" --cell-types-column "${cell_types_column}" --output-path "${output_tbl_path}" --plot-path "${plot_path}" --confusion-table "${confusion_table}"
+        scpred_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --output-path "${output_tbl_path}"  
+
+        #if $test_labels
+        --test-labels "${test_labels}" 
+        #end if
+        #if $cell_types_column
+        --cell-types-column "${cell_types_column}"
+        #end if
+        #if $plot_path
+        --plot-path "${plot_path}"
+        #end if
+        #if $confusion_table
+        --confusion-table "${confusion_table}"
+        #end if
+
         ]]></command>
     <inputs>
         <param type="data" name="input_object" label="Input SCE object" format="rdata" help="Input SCE object in .rds format" />