# HG changeset patch
# User ebi-gxa
# Date 1587740935 0
# Node ID d639f4cdd2bd01e7f49b69a543959fea4b6ad18c
# Parent  dad2fc72913aa1eba815971b3ed1e553c7fe17c5
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r dad2fc72913a -r d639f4cdd2bd ct_build_cell_ontology_dict.xml
--- a/ct_build_cell_ontology_dict.xml	Thu Apr 16 08:48:22 2020 +0000
+++ b/ct_build_cell_ontology_dict.xml	Fri Apr 24 15:08:55 2020 +0000
@@ -10,7 +10,20 @@
             cp '$sdrf' input_dir/;
         #end for
 
-        build_cell_ontology_dict.R --input-dir input_dir --condensed-sdrf "${condensed_sdrf}" --barcode-col-name "${barcode_col_name}" --cell-label-col-name "${cell_label_col_name}" --cell-ontology-col-name "${cell_ontology_col_name}" --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}" ]]></command>
+        build_cell_ontology_dict.R --input-dir input_dir  --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}"
+        #if $condensed_sdrf
+        --condensed-sdrf "${condensed_sdrf}" 
+        #end if
+        #if $barcode_col_name
+        --barcode-col-name "${barcode_col_name}"
+        #end if
+        #if $cell_label_col_name
+        --cell-label-col-name "${cell_label_col_name}"
+        #end if
+        #if $cell_ontology_col_name
+        --cell-ontology-col-name "${cell_ontology_col_name}" 
+        #end if
+         ]]></command>
     <inputs>
         <param type="data" name="input_sdrfs" label="Input SDRF tables" multiple="true" format="tsv" help="Input SDRF tables" />
         <param type="boolean" name="condensed_sdrf" checked="false" label="Condensed SDRF" help="Are the supplied SDRFs of condensed format?" />