diff scpred_train_test_split.xml @ 3:c48d7623f7f8 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"

--- a/scpred_train_test_split.xml	Fri Apr 24 15:18:22 2020 +0000
+++ b/scpred_train_test_split.xml	Wed Apr 29 16:36:54 2020 +0000
@@ -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" />