--- a/tracegroomer.xml	Thu Aug 22 18:45:15 2024 +0000
+++ b/tracegroomer.xml	Tue Sep 03 19:22:57 2024 +0000
@@ -37,20 +37,20 @@
             $fractions_stomp_values
             $subtract_blankavg
             $under_detection_limit_set_nan
-            -ox 'tsv' &&
+            -ox $output_files_extension &&
             #if $type_of_file.type_of_file_selector == "IsoCor_out_tsv":
-                cp -rf '${AbundanceCorrected}.tsv' '${AbundanceCorrected}' &&
-                cp -rf '${MeanEnrichment13C}.tsv' '${MeanEnrichment13C}' &&
-                cp -rf '${IsotopologuesProp}.tsv' '${IsotopologuesProp}' &&
-                cp -rf '${IsotopologuesAbs}.tsv' '${IsotopologuesAbs}'
+                cp -rf '${AbundanceCorrected}.${output_files_extension}' '${AbundanceCorrected}' &&
+                cp -rf '${MeanEnrichment13C}.${output_files_extension}' '${MeanEnrichment13C}' &&
+                cp -rf '${IsotopologuesProp}.${output_files_extension}' '${IsotopologuesProp}' &&
+                cp -rf '${IsotopologuesAbs}.${output_files_extension}' '${IsotopologuesAbs}'
             #else if $type_of_file.type_of_file_selector == "rule_tsv":
-                cp -rf '${Absolute_isotopologue_abundances}.tsv' '${Absolute_isotopologue_abundances}'
+                cp -rf '${Absolute_isotopologue_abundances}.${output_files_extension}' '${Absolute_isotopologue_abundances}'
             #else if $type_of_file.type_of_file_selector == "generic_xlsx":
-                cp -rf '${sheetname}.tsv' '${isotopologuesCorrValues}'
+                cp -rf '${sheetname}.${output_files_extension}' '${isotopologuesCorrValues}'
             #else:
-                cp -rf '${raw_abundance_sheet_name}.tsv' '${rawAbundances}' &&
-                cp -rf '${frac_contribution_sheet_name}.tsv' '${FracContribution_C}' &&
-                cp -rf '${corrected_isotopologues_sheet_name}.tsv' '${CorrectedIsotopologues}'
+                cp -rf '${raw_abundance_sheet_name}.${output_files_extension}' '${rawAbundances}' &&
+                cp -rf '${frac_contribution_sheet_name}.${output_files_extension}' '${FracContribution_C}' &&
+                cp -rf '${corrected_isotopologues_sheet_name}.${output_files_extension}' '${CorrectedIsotopologues}'
             #end if
 
     ]]></command>
@@ -98,7 +98,7 @@
         <expand macro="advanced_options"/>
     </inputs>
     <outputs>
-        <data label="Corrected isotope abundances" name="AbundanceCorrected" format="tabular">
+        <data label="Total metabolite abundances" name="AbundanceCorrected" format="tabular">
             <filter>type_of_file['type_of_file_selector'] == 'IsoCor_out_tsv'</filter>
         </data>
         <data label="Mean enrichment data" name="MeanEnrichment13C" format="tabular">
@@ -133,11 +133,11 @@
             <param name="type_of_file_selector" value="IsoCor_out_tsv"/>
             <section name="advanced_options">
                 <param name="isosprop_min_admitted" ftype="float"  value='-0.5'/>
-                <param name="alternative_div_amount_material" ftype="boolean"  value='true'/>
-                <param name="div_isotopologues_by_amount_material" ftype="boolean"  value='true'/>
-                <param name="isotopologues_preview" ftype="boolean"  value='false'/>
-                <param name="fractions_stomp_values" ftype="boolean"  value='true'/>
-                <param name="subtract_blankavg" ftype="boolean"  value='true'/>
+                <param name="alternative_div_amount_material" ftype="boolean" value='true'/>
+                <param name="div_isotopologues_by_amount_material" ftype="boolean" value='true'/>
+                <param name="isotopologues_preview" ftype="boolean" value='false'/>
+                <param name="fractions_stomp_values" ftype="boolean" value='true'/>
+                <param name="subtract_blankavg" ftype="boolean" value='true'/>
                 <param name="under_detection_limit_set_nan" ftype="boolean"  value='true'/>
             </section>
             <output file="AbundanceCorrected.tsv" name="AbundanceCorrected" ftype="tabular"/>
@@ -325,7 +325,7 @@
     - Normalize by an internal standard (present in your data) at choice.
     - Print a preview of isotopologues values.
 
-Please visit our Wiki page (https://github.com/cbib/TraceGroomer/wiki) for more information, and how to get help.
+Please visit our Wiki page (https://github.com/cbib/TraceGroomer/wiki) for more information, and how to get help. Details of advanced options available in https://github.com/cbib/TraceGroomer/wiki/4-Advanced-options.
 
  ]]>
     </help>