Merge pull request galaxyproject#5742 from bdartigues/dimet_update_to…

…_0_2_0 Upgrade DIMet to 0.2.1 + add new tool dimet_bivariate_analysis.xml + …
pavanvidem · Feb 15, 2024 · 30fe10a · 30fe10a
2 parents f9a5ca5 + 31b52e5
commit 30fe10a
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diff --git a/tools/dimet/dimet_abundance_plot.xml b/tools/dimet/dimet_abundance_plot.xml
@@ -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 @@ The output consists of bar-plot figures, one by each metabolite, and one legend
 
 **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>

diff --git a/tools/dimet/dimet_bivariate_analysis.xml b/tools/dimet/dimet_bivariate_analysis.xml
diff --git a/tools/dimet/dimet_differential_analysis.xml b/tools/dimet/dimet_differential_analysis.xml
@@ -13,7 +13,7 @@
     @INIT_DIFF_ANALYSIS@
     @INIT_STAT_TEST@
     @INIT_GROUPS@
-    @INIT_COMPARISONS@
+    @INIT_DIFF_ANALYSIS_COMPARISONS@
     HYDRA_FULL_ERROR=1 python -m dimet
         -cp '$__new_file_path__/config'
         '++hydra.run.dir=differential_analysis'
@@ -43,7 +43,7 @@
          '++analysis.method.impute_values=${impute_values}'
          '++analysis.statistical_test=${statistical_test}'
          '++analysis.dataset.subfolder='
-         '++analysis.dataset.conditions=${conds}'
+         '++analysis.dataset.conditions=${conditions}'
          #if $metadata_path:
              '++analysis.dataset.metadata=metadata'
          #end if
@@ -68,7 +68,7 @@
     ]]></command>
     <inputs>
         <expand macro="input_parameters_diff_analysis"/>
-        <expand macro="conditions"/>
+        <expand macro="factor_list"/>
         <expand macro="timepoint"/>
         <expand macro="correction_method"/>
         <param name="qualityDistanceOverSpan" type="float" min="-1.0" max="-0.1" value="-0.3" label="quality Distance Over Span" help="Default value is -0.3."/>
@@ -85,9 +85,15 @@
             <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/>
             <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
             <param name="correction_method" value="bonferroni"/>
+            <param name="statistical_test_type" value="parametric"/>
             <param name="stat_test" value="Tt"/>
             <param name="qualityDistanceOverSpan" value="-0.3"/>
-            <param name="conditions" value='Control,L-Cycloserine'/>
+            <repeat name="factor_list">
+                <param name="condition" value="Control"/>
+            </repeat>
+            <repeat name="factor_list">
+                <param name="condition" value="L-Cycloserine"/>
+            </repeat>
             <param name="timepoint" value='T0,T2h'/>
              <output_collection name="report" type="list" count="4">
                 <element file="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv"  name="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>
@@ -283,12 +289,17 @@ To use with caution in case of important dispersion of your intra-group values.
 
 There exist hints on use that will guide you, next to the parameters.
 
+For more information about the implemented statistical tests, please visit:  https://github.com/cbib/DIMet/wiki/2-Statistical-tests
+
+The output files are explained in https://github.com/cbib/DIMet/wiki/3-Output
+
+
 
 **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>

diff --git a/tools/dimet/dimet_differential_multigroup_analysis.xml b/tools/dimet/dimet_differential_multigroup_analysis.xml
@@ -11,10 +11,9 @@
     <command detect_errors="exit_code"><![CDATA[
     @INIT_CONFIG@
     @INIT_DIFF_MULTIGROUP_ANALYSIS@
-    @INIT_STAT_TEST@
     @INIT_DATATYPES@
     @INIT_GROUPS@
-    @INIT_CONDITIONS@
+    @INIT_PLOT_CONDITIONS@
     @INIT_TIMEPOINTS@
     @INIT_MULTIGROUP_COMPARISONS@
     HYDRA_FULL_ERROR=1 python -m dimet
@@ -36,16 +35,14 @@
             datatypes:${datatypes_avail}
         }'
         '++analysis.method.datatypes=${datatypes_avail}'
-        '++analysis.method.qualityDistanceOverSpan='${qualityDistanceOverSpan}''
         '++analysis.timepoints=${timepoints}'
         '++analysis.conditions=${comparisons}'
         '++analysis.dataset.label='
-        '++analysis.statistical_test=${statistical_test}'
         '++analysis.method.correction_method=${correction_method}'
         '++analysis.method.impute_values=${impute_values}'
         '++analysis.dataset.subfolder='
         '++analysis.method.grouping=${groups}'
-        '++analysis.dataset.conditions=${conds}'
+        '++analysis.dataset.conditions=${conditions}'
          #if $metadata_path:
              '++analysis.dataset.metadata=metadata'
          #end if
@@ -69,12 +66,11 @@
     @REMOVE_CONFIG@
     ]]></command>
     <inputs>
-        <expand macro="input_parameters_diff_analysis"/>
-        <expand macro="conditions_multigroup"/>
+        <expand macro="input_parameters_multi_diff_analysis"/>
+        <expand macro="plot_factor_list"/>
         <expand macro="timepoint_multigroup"/>
         <expand macro="compartments"/>
         <expand macro="correction_method"/>
-        <param name="qualityDistanceOverSpan" type="float" min="-1.0" max="-0.1" value="-0.3" label="quality Distance Over Span" help="Default value is -0.3."/>
     </inputs>
 
     <outputs>
@@ -87,10 +83,16 @@
             <param name="data_input_selector" value="abundance" />
             <param name="abundance_file" ftype="tabular" value="rawAbundances3.csv"/>
             <param name="metadata_path" ftype="tabular" value="example3_metadata.csv"/>
-            <param name="stat_test" value="Tt"/>
             <param name="correction_method" value="bonferroni"/>
-            <param name="qualityDistanceOverSpan" value="-0.3"/>
-            <param name="conditions" value="Control,Cond1,Cond2"/>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="Control"/>
+            </repeat>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="Cond1"/>
+            </repeat>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="Cond2"/>
+            </repeat>
             <param name="timepoint" value="T0h,T2h"/>
             <param name="compartments" value="cell"/>
 
@@ -104,7 +106,7 @@ This module is part of DIMet: Differential analysis of Isotope-labeled targeted
 
     **Input data files**
 
-This tool computes the Kruskall Wallis test over 3 or more groups,
+This tool computes the Kruskal-Wallis test over 3 or more groups,
 to evaluate if at least one group is significantly different to the other groups (H0: median of all of the groups is equal). For illustration see the section **Metadata File Information** which contains three conditions: Control, Core_mass and Edge_tissue, across one single time point, thus 3 groups (number-of-groups-in-my-data = number-of-conditions x number-of-timepoints)).
 
 This tool requires (at max.) 5 tab-delimited .csv files as inputs. There are two types of files:
@@ -247,11 +249,15 @@ You can precise how you want your analysis to be executed, with the parameters:
 
 There exist hints on use that will guide you, next to the parameters.
 
+For more information about the implemented statistical tests, please visit:  https://github.com/cbib/DIMet/wiki/2-Statistical-tests
+
+The output files are explained in https://github.com/cbib/DIMet/wiki/3-Output
+
 **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>

diff --git a/tools/dimet/dimet_enrichment_plot.xml b/tools/dimet/dimet_enrichment_plot.xml
@@ -11,7 +11,7 @@
     <command detect_errors="exit_code"><![CDATA[
     @INIT_CONFIG@
     @INIT_ENRICHMENT_PLOT@
-    @INIT_CONDITIONS@
+    @INIT_PLOT_CONDITIONS@
     @INIT_TIMEPOINTS@
     @INIT_ENRICHMENT_METABOLITES@
     HYDRA_FULL_ERROR=1 python -m dimet
@@ -29,7 +29,7 @@
                 _target_: dimet.method.MeanEnrichmentLinePlotConfig,
                 label: mean_enrichment_line_plot,
                 name: "Generate mean enrichment line plots",
-                palette_condition: muted,
+                palette_condition: ${output_options.palette},
                 palette_metabolite: auto_multi_color,
                 xaxis_title: ${output_options.xaxis_title},
                 alpha: ${output_options.alpha},
@@ -45,7 +45,7 @@
         '++analysis.dataset.label='
         '++analysis.timepoints=${timepoints}'
         '++analysis.dataset.subfolder='
-        '++analysis.dataset.conditions=${conds}'
+        '++analysis.dataset.conditions=${conditions}'
 
         #if $metadata_path:
              '++analysis.dataset.metadata=metadata'
@@ -57,7 +57,7 @@
     ]]></command>
     <inputs>
         <expand macro="input_parameters_enrichment"/>
-        <expand macro="conditions"/>
+        <expand macro="plot_factor_list"/>
         <expand macro="timepoint"/>
         <expand macro="compartments_enrichment"/>
         <expand macro="enrichment_metabolites_list"/>
@@ -66,6 +66,7 @@
                 <option value="pdf">Pdf</option>
                 <option value="svg">Svg</option>
             </param>
+            <expand macro="palette"/>
             <param name="color_lines_by" type="select" value="condition" display="radio" label="Select color for lines" help="Please enter at max 1 format">
                 <option value="condition">Condition</option>
                 <option value="metabolite">Metabolite</option>
@@ -97,7 +98,12 @@
         <test>
             <param name="me_or_frac_contrib_file" ftype="tabular" value="FracContribution_C.csv"/>
             <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
-            <param name="conditions" value='Control,L-Cycloserine'/>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="Control"/>
+            </repeat>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="L-Cycloserine"/>
+            </repeat>
             <param name="timepoint" value='T0,T2h'/>
             <param name="compartments" value='cell,med'/>
             <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/>
@@ -229,9 +235,9 @@ The output consists of line-plot figures, one by each metabolite.
 
 **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>

diff --git a/tools/dimet/dimet_isotopologues_plot.xml b/tools/dimet/dimet_isotopologues_plot.xml
@@ -11,7 +11,7 @@
     <command detect_errors="exit_code"><![CDATA[
     @INIT_CONFIG@
     @INIT_ISOTOPOLOGUE_PLOT@
-    @INIT_CONDITIONS@
+    @INIT_PLOT_CONDITIONS@
     @INIT_TIMEPOINTS@
     HYDRA_FULL_ERROR=1 python -m dimet
         -cp '$__new_file_path__/config'
@@ -46,7 +46,7 @@
         '++analysis.width_each_stack='${output_options.width_each_stack}''
         '++analysis.method.height_each_stack='${output_options.height_each_stack}''
         '++analysis.dataset.subfolder='
-        '++analysis.dataset.conditions=${conds}'
+        '++analysis.dataset.conditions=${conditions}'
         '++x_text='metabolites''
 
         #if $metadata_path:
@@ -59,7 +59,7 @@
     ]]></command>
     <inputs>
         <expand macro="input_parameters_isotopologue"/>
-        <expand macro="conditions"/>
+        <expand macro="plot_factor_list"/>
         <expand macro="timepoint"/>
         <section name="output_options" title="Output options">
             <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format">
@@ -98,7 +98,12 @@
         <test>
             <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
             <param name="isotop_prop_file" ftype="tabular" value="CorrectedIsotopologues_reduced.csv"/>
-            <param name="conditions" value='Control,L-Cycloserine'/>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="Control"/>
+            </repeat>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="L-Cycloserine"/>
+            </repeat>
             <param name="timepoint" value='T0,T2h'/>
             <section name="output_options">
                 <param name="figure_format" value="svg"/>
@@ -242,9 +247,9 @@ The output consist of stacked-bar figures, one by each metabolite, and one legen
 
 **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>