# HG changeset patch
# User iuc
# Date 1725391394 0
# Node ID 5147f08d67c93013b8a2a5e4fe82d5badb9f6178
# Parent  ea6ea4029c47025288e7eda64111c5a94a76e563
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2

diff -r ea6ea4029c47 -r 5147f08d67c9 macros.xml
--- a/macros.xml	Thu Aug 22 18:45:34 2024 +0000
+++ b/macros.xml	Tue Sep 03 19:23:14 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.1.4</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">tracegroomer</requirement>
@@ -81,20 +81,24 @@
         </conditional>
     </xml>
     <xml name="advanced_options">
-        <section name="advanced_options" title="Advanced options" expanded="false">
-
-            <param name="alternative_div_amount_material" type="boolean"  truevalue="--alternative_div_amount_material" falsevalue="" label="alternative isotopologues division by amount material" help="In the normalisation by the amount of material, not only the division of the given absolute values by these amounts is performed, but also the product of the resulting quotients and the averaged amount of material is computed"/>
-            <param name="div_isotopologues_by_amount_material" type="boolean" truevalue="--div_isotopologues_by_amount_material" falsevalue="" label="isotopologues by amount material" help="Apply normalization by the amount of material at the level of isotopologue absolute values. Immediately after this, and before any other computation, tracegroomer re-computes all derived (thus normalized) metrics"/>
-            <param name="isotopologues_preview" type="boolean" truevalue="--isotopologues_preview" falsevalue="" label="Plot isotopologue" help="Generate simple plots that give a general overview of the isotopologue proportions given by the user. Performs a scatter plot of the individual isotopologue proportions for all metabolites, as well as a plot of the sums of isotopologue proportions (the sum must be equal to 1 for each metabolite and sample)"/>
-            <param name="fractions_stomp_values" type="boolean" truevalue="--fractions_stomp_values" falsevalue="" label="Stomps fractional contributions" help="Stomps fractional contributions (synonym: mean enrichment), and isotopologue proportions, to max 1.0 and min 0.0"/>
-            <param name="subtract_blankavg" type="boolean" truevalue="--subtract_blankavg" falsevalue="" label="" help="from samples' abundances, subtracts the average of the blanks for all metabolites across all samples. Note that the Internal Standards are not subjected to this operation, as recommended by VIB platform"/>
-            <param name="under_detection_limit_set_nan" type="boolean" truevalue="--under_detection_limit_set_nan" falsevalue="" label="Limit Of Detection" help="The Limit Of Detection, LOD, corresponds to the averaged blanks abundance values, multiplied by three times the blanks standard deviation. By default, any value that is strictly inferior to its corresponding LOD, is converted into NaN"/>
+        <section name="advanced_options" title="Advanced options" expanded="false" help="Default values explained in our Wiki page (link at the end of the Help section)">
+            <param name="div_isotopologues_by_amount_material" type="boolean" truevalue="--div_isotopologues_by_amount_material" checked="true" falsevalue="--no-div_isotopologues_by_amount_material" label="isotopologues division by amount material" help="Apply normalization by the amount of material at the level of isotopologue absolute values. Immediately after this, and before any other computation, tracegroomer re-computes all derived (thus normalized) metrics"/>
+            <param name="alternative_div_amount_material" type="boolean"  truevalue="--alternative_div_amount_material" checked="true" falsevalue="--no-alternative_div_amount_material" label="alternative division of values by amount material" help="In the normalisation by the amount of material, not only the division of the given absolute values by these amounts is performed, but also the product of the resulting quotients 'q' and the averaged amount of material 'a' (q x a) so abundance units are preserved"/>
+            <param name="isotopologues_preview" type="boolean" truevalue="--isotopologues_preview" checked="false" falsevalue="--no-isotopologues_preview" label="Plot isotopologues" help="Generate simple plots that give a general overview of the isotopologue proportions given by the user. Performs a scatter plot of the individual isotopologue proportions for all metabolites, as well as a plot of the sums of isotopologue proportions (the sum must be equal to 1 for each metabolite and sample)"/>
+            <param name="fractions_stomp_values" type="boolean" truevalue="--fractions_stomp_values" checked="true" falsevalue="--no-fractions_stomp_values" label="Stomp fractional contributions" help="Stomps fractional contributions (synonym: mean enrichment), and isotopologue proportions, to max 1.0 and min 0.0"/>
+            <param name="subtract_blankavg" type="boolean" truevalue="--subtract_blankavg" checked="true" falsevalue="--no-subtract_blankavg" label="Subtract blanks avg (VIB input only)" help="from samples' abundances, subtracts the average of the blanks for all metabolites across all samples. Note that the Internal Standards are not subjected to this operation, as recommended by VIB platform"/>
+            <param name="under_detection_limit_set_nan" type="boolean" truevalue="--under_detection_limit_set_nan" checked="true" falsevalue="--no-under_detection_limit_set_nan" label="Limit Of Detection (VIB input only)" help="The Limit Of Detection, LOD, corresponds to the averaged blanks abundance values, multiplied by three times the blanks standard deviation. By default, any value that is strictly inferior to its corresponding LOD, is converted into NaN"/>
             <param name="use_internal_standard" type="text" optional="true" help="The name of the internal standard, which is a compound or metabolite that has been stated as reference signal. By providing this name, the normalization by the internal standard is automatically performed" label="internal standard" />
             <param name="isosprop_min_admitted" type="float" min="-1.0" max="1.0" value="-0.5" label="isotopologues cutoff" help="Metabolites whose isotopologue proportions are less or equal to this cutoff, are removed"/>
+            <param name="output_files_extension" type="select" value="tsv" display="radio" label="output files extension" help="Note that tab delimited files are always produced, for any chosen extension">
+                <option value="tsv">tsv</option>
+                <option value="csv">csv</option>
+            </param>
         </section>
     </xml>
     <xml name="citations">
         <citations>
+            <citation type="doi">10.1093/bioinformatics/btae282</citation>
             <citation type="bibtex">
                 @software{Galvis_Rodriguez_DIMet,
                     author = {Galvis Rodriguez, Johanna  and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},
diff -r ea6ea4029c47 -r 5147f08d67c9 tracegroomer.xml
--- a/tracegroomer.xml	Thu Aug 22 18:45:34 2024 +0000
+++ b/tracegroomer.xml	Tue Sep 03 19:23:14 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>