# HG changeset patch
# User recetox
# Date 1641914037 0
# Node ID 364976b9aba6bf16efa5ef7d0fda8d8fd1095fd5
# Parent  0a08bed94964a04684f3da3d00fa8015179baba1
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 67040e686204e86c07ec46ca90129e50e40eb737"

diff -r 0a08bed94964 -r 364976b9aba6 formatter.py
--- a/formatter.py	Sat Oct 30 13:48:25 2021 +0000
+++ b/formatter.py	Tue Jan 11 15:13:57 2022 +0000
@@ -73,8 +73,8 @@
     Returns:
         DataFrame: Joined dataframe on compounds containing scores an matches in long format.
     """
-    matches = read_csv(matches_filename, sep='\t', index_col=0)
-    scores = read_csv(scores_filename, sep='\t', index_col=0)
+    matches = read_csv(matches_filename, sep=None, index_col=0)
+    scores = read_csv(scores_filename, sep=None, index_col=0)
 
     scores_long = create_long_table(scores, 'score')
     matches_long = create_long_table(matches, 'matches')
@@ -113,8 +113,11 @@
 
 @cli.resultcallback()
 def write_output(result: DataFrame, scores_filename, matches_filename, output_filename):
+    input_file = read_csv(scores_filename, sep=None, iterator=True)
+    sep = input_file._engine.data.dialect.delimiter
+
     result = result.reset_index().rename(columns={'level_0': 'query', 'compound': 'reference'})
-    result.to_csv(output_filename, sep="\t", index=False)
+    result.to_csv(output_filename, sep=sep, index=False)
 
 
 if __name__ == '__main__':
diff -r 0a08bed94964 -r 364976b9aba6 matchms_formatter.xml
--- a/matchms_formatter.xml	Sat Oct 30 13:48:25 2021 +0000
+++ b/matchms_formatter.xml	Tue Jan 11 15:13:57 2022 +0000
@@ -31,8 +31,8 @@
     </configfiles>
 
     <inputs>
-        <param label="Scores Table" name="scores" type="data" format="tsv" help="Scores output table." />
-        <param label="Matches Table" name="matches" type="data" format="tsv" help="Scores output table." />
+        <param label="Scores Table" name="scores" type="data" format="csv,tsv" help="Scores output table." />
+        <param label="Matches Table" name="matches" type="data" format="csv,tsv" help="Scores output table." />
 
         <conditional name="method">
             <param name="selection" type="select" label="Formatting method">
@@ -52,7 +52,7 @@
 
     </inputs>
     <outputs>
-        <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format="tsv" />
+        <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format_source="scores" />
     </outputs>
 
     <tests>