# HG changeset patch
# User ebi-gxa
# Date 1587741633 14400
# Node ID 7086be9e707ed6d29829d57f8c4f1a6ac4365215
# Parent  406d293e567e81ee6e5ef535177a2a4f842bf48b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r 406d293e567e -r 7086be9e707e ct_build_cell_ontology_dict.xml
--- a/ct_build_cell_ontology_dict.xml	Wed Apr 08 11:35:35 2020 -0400
+++ b/ct_build_cell_ontology_dict.xml	Fri Apr 24 11:20:33 2020 -0400
@@ -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?" />
diff -r 406d293e567e -r 7086be9e707e ct_macros.xml
--- a/ct_macros.xml	Wed Apr 08 11:35:35 2020 -0400
+++ b/ct_macros.xml	Fri Apr 24 11:20:33 2020 -0400
@@ -29,7 +29,8 @@
             url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git},
           }
         </citation>
+        <citation type="doi">10.1101/2020.04.08.032698</citation>
         <yield />
       </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>