--- a/dimet_abundance_plot.xml	Tue Jan 23 14:57:41 2024 +0000
+++ b/dimet_abundance_plot.xml	Thu Feb 15 12:51:47 2024 +0000
@@ -11,7 +11,7 @@
     <command detect_errors="exit_code"><![CDATA[
     @INIT_CONFIG@
     @INIT_ABUNDANCE_PLOT@
-    @INIT_CONDITIONS@
+    @INIT_ABUNDANCE_PLOT_CONDITIONS@
     @INIT_TIMEPOINTS@
     @INIT_ENRICHMENT_METABOLITES@
     HYDRA_FULL_ERROR=1 python -m dimet
@@ -35,6 +35,7 @@
                 height_each_subfig: '${output_options.height_each_subfig}',
                 palette:${output_options.palette},
                 as_grid:${output_options.as_grid},
+                x_text_modify_as:null,
                 do_stripplot:${output_options.do_stripplot},
                 figure_format:${output_options.figure_format}
             },
@@ -44,7 +45,7 @@
         '++analysis.dataset.label='
         '++analysis.timepoints=${timepoints}'
         '++analysis.dataset.subfolder='
-        '++analysis.dataset.conditions=${conds}'
+        '++analysis.dataset.conditions=${conditions}'
         #if $metadata_path:
              '++analysis.dataset.metadata=metadata'
         #end if
@@ -55,18 +56,12 @@
     ]]></command>
     <inputs>
         <expand macro="input_parameters_abundance"/>
-        <expand macro="conditions"/>
+        <expand macro="plot_abundance_factor_list"/>
         <expand macro="timepoint"/>
         <expand macro="compartments_abundance"/>
         <expand macro="abundance_metabolites_list"/>
         <section name="output_options" title="Output options">
-            <param name="palette" type="select" value="pastel" display="radio" label="Select palette colormap to apply to abundance plot" help="Please enter at max 1 statistical test by file">
-                <option value="pastel">pastel</option>
-                <option value="Set1">Set1</option>
-                <option value="Set2">Set2</option>
-                <option value="Set3">Set3</option>
-                <option value="Dark2">Dark2</option>
-            </param>
+            <expand macro="palette"/>
             <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format">
                 <option value="pdf">Pdf</option>
                 <option value="svg">Svg</option>
@@ -93,7 +88,9 @@
         <test>
             <param name="abundance_file" ftype="tabular" value="AbundanceCorrected.csv"/>
             <param name="metadata_path" ftype="tabular" value="example1_metadata.csv"/>
-            <param name="conditions" value='sgLDHA'/>
+            <repeat name="plot_abundance_factor_list">
+                <param name="condition" value="sgLDHA"/>
+            </repeat>
             <param name="timepoint" value='T0,T24'/>
             <param name="compartments" value='endo'/>
             <param name="metabolites_list" value="Fru1P"/>
@@ -223,9 +220,9 @@
 
 **Available data for testing**
 
-You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent
+You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
 files for you are located in the subfolders inside the data folder).
-You can also use the minimal data examples from https://zenodo.org/record/8380706
+You can also use the minimal data examples from https://zenodo.org/record/10579891
 
  ]]>
     </help>