# HG changeset patch
# User ebi-gxa
# Date 1588178612 14400
# Node ID a6d66c9953ed6a53b4a3e208a70158467a4fd6c3
# Parent  148fae20fe6474531aa25a9d8bcb470407236599
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"

diff -r 148fae20fe64 -r a6d66c9953ed scpred_train_test_split.xml
--- a/scpred_train_test_split.xml	Fri Apr 24 11:28:11 2020 -0400
+++ b/scpred_train_test_split.xml	Wed Apr 29 12:43:32 2020 -0400
@@ -1,11 +1,20 @@
-<tool id="scpred_traint_test_split" name="Scpred train-test split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="scpred_traint_test_split" name="Scpred train-test split" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>CPM normalise and partition into train/test data</description>
     <macros>
         <import>scpred_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scpred_train_test_split.R --input-sce-object "${input_sce_object}" --normalised-counts-slot "${norm_counts_slot}" --training-matrix "${training_mat}" --test-matrix "${test_mat}" --cell-types-column "${cell_types_col}" --training-labels "${training_labs}" --test-labels "${test_labs}" --training-ratio "${training_ratio}" ]]></command>
+        scpred_train_test_split.R --input-sce-object "${input_sce_object}"  --training-matrix "${training_mat}" --test-matrix "${test_mat}"  --training-labels "${training_labs}"  --cell-types-column "${cell_types_col}" --test-labels "${test_labs}" 
+
+        #if $norm_counts_slot
+        --normalised-counts-slot "${norm_counts_slot}"
+        #end if
+        #if $training_ratio
+        --training-ratio "${training_ratio}" 
+        #end if
+
+        ]]></command>
     <inputs>
         <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" />
         <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" />