# HG changeset patch
# User ebi-gxa
# Date 1587994002 14400
# Node ID a565cf41330bdb5b92815dc4d60a6982c216d60c
# Parent  dc68e75e8ae35cd5cc13d30ee80b7c5ff4d7e0e3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"

diff -r dc68e75e8ae3 -r a565cf41330b ct_combine_tool_outputs.xml
--- a/ct_combine_tool_outputs.xml	Fri Apr 24 11:19:44 2020 -0400
+++ b/ct_combine_tool_outputs.xml	Mon Apr 27 09:26:42 2020 -0400
@@ -10,15 +10,20 @@
           cp '$table' input_dir/;
         #end for
 
-        combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --exclusions "${exclusions}" --scores "${scores}" --output-table "${output_table}" ]]></command>
+        combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --scores "${scores}" --output-table "${output_table}" 
+
+        #if $exclusions
+        --exclusions "${exclusions}"
+        #end if
+        ]]></command>
     <inputs>
-        <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="tsv" help="Standardised tables obtained from multiple classifiers" />
+        <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="txt" help="Standardised tables obtained from multiple classifiers" />
         <param type="integer" name="top_labels_num" label="Number of top labels" value='3' help="Number of top labels to select" />
         <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" />
         <param type="boolean" name="scores" label="scores" checked="false" help="Are scores included into the tool outpus?" />
     </inputs>
     <outputs>
-        <data name="output_table" format="tsv" />
+        <data name="output_table" format="txt" />
     </outputs>
     <tests>
         <test>