# HG changeset patch
# User ebi-gxa
# Date 1588178101 0
# Node ID 39b208cca9f11755fc61eacc1793b285124f9f39
# Parent  0cd6c851ccfeef25e95447301f06a18d210feec9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"

diff -r 0cd6c851ccfe -r 39b208cca9f1 scpred_preprocess_data.xml
--- a/scpred_preprocess_data.xml	Mon Apr 27 13:22:44 2020 +0000
+++ b/scpred_preprocess_data.xml	Wed Apr 29 16:35:01 2020 +0000
@@ -1,11 +1,20 @@
-<tool id="scpred_preprocess_data" name="Scpred pre-process" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="scpred_preprocess_data" name="Scpred pre-process" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>Pre-process input dataset (no train/test split)</description>
     <macros>
         <import>scpred_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scpred_preprocess_data.R --input-sce-object "${input_sce_object}" --normalised-counts-slot "${norm_counts_slot}" --output-matrix-object "${output_mat_object}" --output-labels "${output_labels}" ]]></command>
+        scpred_preprocess_data.R --input-sce-object "${input_sce_object}" --output-matrix-object "${output_mat_object}" 
+
+        #if $norm_counts_slot
+        --normalised-counts-slot "${norm_counts_slot}"
+        #end if
+        #if $output_labels
+        --output-labels "${output_labels}"
+        #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" />